NM_000256.3(MYBPC3):c.3624delC
criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.
Pathogenic (10)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_000256.3(MYBPC3):c.3624delC
Variation ID: 42727 Accession: VCV000042727.38
- Type and length
-
Deletion, 1 bp
- Location
-
Cytogenetic: 11p11.2 11: 47332569 (GRCh38) [ NCBI UCSC ] 11: 47354120 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Feb 24, 2015 Aug 4, 2026 Oct 13, 2025 - HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000256.3:c.3624delC MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NC_000011.10:g.47332572del NC_000011.9:g.47354123del NG_007667.1:g.25134del LRG_386:g.25134del LRG_386t1:c.3624del LRG_386p1:p.Lys1209fs - Protein change
- -
- Other names
- -
- Canonical SPDI
- NC_000011.10:47332568:GGGG:GGG
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
- -
- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
| MYBPC3 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
4727 | 4749 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
|
Oct 9, 2025 | RCV000158405.12 | |
| Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
|
Oct 13, 2025 | RCV000231140.20 | |
| Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
|
Mar 26, 2024 | RCV000770322.6 | |
| Pathogenic (1) |
criteria provided, single submitter
|
Oct 18, 2021 | RCV001194064.2 | |
| Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
|
Oct 19, 2020 | RCV004786297.4 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
Expand all rows
Collapse all rows
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
|---|---|---|---|---|---|
|
Pathogenic
(Apr 06, 2018)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
Blueprint Genetics
Accession: SCV000927618.1
First in ClinVar: Jul 24, 2019 Last updated: Jul 24, 2019
Comment:
Patient analyzed with Hypertrophic Cardiomyopathy (HCM) Panel
|
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Mar 23, 2020)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypertrophic cardiomyopathy
(Autosomal dominant inheritance)
|
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000059253.6
First in ClinVar: May 03, 2013 Last updated: Jul 03, 2020 |
Comment:
show
The p.Lys1209SerfsX28 variant in MYBPC3 (also reported as p.Pro1208fs in the literature) has been identified in at least 10 unrelated individuals with hypertrophic cardiomyopathy (HCM; including an individual who also carried a disease causing variant in another HCM associated gene) and segregated with disease in at least 2 affected relatives from 2 families (Li 2009, Zou 2013, Liu 2013, Liu 2015, LMM data). It has also been reported by other clinical laboratories in ClinVar (Variation ID 42727) and has been identified in 0.005% (1/19456) of East Asian chromosomes and 1/127178 European chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 1209 and leads to a premature termination codon 28 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Loss of function of the MYBPC3 gene is an established disease mechanism in autosomal dominant HCM. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant HCM. ACMG/AMP Criteria applied: PVS1, PS4_Strong. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Number of individuals with the variant: 12
|
|
|
Pathogenic
(May 31, 2022)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Cardiomyopathy |
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario
Accession: SCV000901756.4
First in ClinVar: May 06, 2019 Last updated: Mar 11, 2023 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Oct 09, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
GeneDx
Accession: SCV000208340.16
First in ClinVar: Feb 24, 2015 Last updated: Oct 25, 2025 |
Comment:
show
Not observed at significant frequency in large population cohorts (gnomAD); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 23283745, 28498465, 28614222, 26914223, 26090888, 27532257, 28241245, 28790153, 28408708, 28615295, 27112610, 37652022, 36578016, 35717150, 33996946, 23711808, 29497013, 33673806, 23549607, 39260623, 40860236, 20128375) (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Oct 18, 2021)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Primary familial hypertrophic cardiomyopathy |
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001363318.2
First in ClinVar: Jun 22, 2020 Last updated: Nov 20, 2021 |
Comment:
show
Variant summary: MYBPC3 c.3624delC (p.Lys1209SerfsX28) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 4e-06 in 246920 control chromosomes (gnomAD). c.3624delC has been reported in the literature in multiple individuals affected with Hypertrophic Cardiomyopathy (example, Liu_2015, and Murphy_2016, Ross_2017, Walsh_2017). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Oct 19, 2020)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypertrophic cardiomyopathy 4 |
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Accession: SCV005398672.1
First in ClinVar: Nov 24, 2024 Last updated: Nov 24, 2024 |
Comment:
show
Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease for this gene. (N) 0108 - This gene is known to be associated with both recessive and dominant disease. Heterozygous variants are frequently reported in adult onset conditions, however recessive inheritance results in a more severe early onset phenotype (OMIM). (N) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (exon 32 of 35). (P) 0251 - Variant is heterozygous. (N) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (2 heterozygotes, 0 homozygotes). (P) 0701 - Comparable variants have very strong previous evidence for pathogenicity. Many other NMD-predicted variants have previously been reported as pathogenic in patients with HCM (ClinVar). (P) 0801 - Strong previous evidence of pathogenicity in unrelated individuals. This variant has previously been reported in multiple individuals with HCM, and it considered to be a common pathogenic variant in the Chinese population (ClinVar, HGMD, PMID: 31941943). (P) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Mar 26, 2024)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Cardiomyopathy |
Color Diagnostics, LLC DBA Color Health
Accession: SCV006064795.1
First in ClinVar: May 03, 2025 Last updated: May 03, 2025 |
Comment:
show
This variant deletes 1 nucleotide in exon 32 of the MYBPC3 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in over 20 individuals affected with hypertrophic cardiomyopathy (PMID: 20128375, 23283745, 23711808, 25132132, 25611685, 26090888, 26914223, 27112610, 28498465, 28615295, 28408708, 28614222, 28790153, 29497013, 30297972, 31941943, 32815737, 32841044, 33673806, 35717150, 36166435, 38489124). It has been shown that this variant segregates with disease in six affected individuals across two families (PMID: 27112610, 28614222). This variant has been identified in 2/278300 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of MYBPC3 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Platform type: NGS
|
|
|
Pathogenic
(-)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypertrophic cardiomyopathy 4 |
Juno Genomics, Hangzhou Juno Genomics, Inc
Accession: SCV005416572.3
First in ClinVar: Nov 30, 2024 Last updated: Oct 05, 2025 |
Comment:
show
Null variant in a gene where loss of function (LOF) is a known mechanism of disease.;The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Oct 13, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypertrophic cardiomyopathy |
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000284244.11
First in ClinVar: Jul 01, 2016 Last updated: Mar 07, 2026 |
Comment:
show
This sequence change creates a premature translational stop signal (p.Lys1209Serfs*28) in the MYBPC3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MYBPC3 are known to be pathogenic (PMID: 19574547). This variant is present in population databases (rs397516030, gnomAD 0.005%). This premature translational stop signal has been observed in individual(s) with MYBPC3-related conditions (PMID: 20128375, 23283745, 23711808, 26090888). This variant is also known as p.Pro1208fs. ClinVar contains an entry for this variant (Variation ID: 42727). For these reasons, this variant has been classified as Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Oct 11, 2016)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
Stanford Center for Inherited Cardiovascular Disease, Stanford University
Accession: SCV000924857.2
First in ClinVar: Jun 29, 2019 Last updated: Aug 04, 2026 |
Observation: 1
Collection method: provider interpretation
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: provider interpretation
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Dec 10, 2019)
N
Not contributing to aggregate classification
|
no assertion criteria provided
|
Hypertrophic cardiomyopathy
(Autosomal dominant inheritance)
|
Agnes Ginges Centre for Molecular Cardiology, Centenary Institute
Accession: SCV001430859.1
First in ClinVar: Aug 22, 2020 Last updated: Aug 22, 2020 |
Comment:
show
The MYBPC Lys1209Serfs*28 has been reported previously in several HCM patients and is absent from the Genome Aggregation Database (http://gnomad.broadinstitute.org/). We identified this MYBPC3 Lys1209Serfs*28 variant in two HCM probands, one of our probands has a family history of HCM, however genetic testing was not possible. Based on the adapted ACMG guidelines (Kelly MA, et al., 2018) this variant results in loss of function of MYBPC3 (PVS1), has been reported in more than 6 unrelated HCM probands (PS4_moderate) and is rare in the general population (PM2), therefore we classify MYBPC3 Lys1209Serfs*28 as a "pathogenic" variant. (less)
Observation: 1
Collection method: research
Allele origin: germline
Affected status: yes
Observation 1
Collection method: research
Allele origin: germline
Affected status: yes
|
|
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| Diagnostic yield from cardiac gene testing for inherited cardiac conditions and re-evaluation of pre-ACMG variants of uncertain significance. | Murphy J | Irish journal of medical science | 2024 | PMID: 38489124 |
| Genomic findings of hypertrophic and dilated cardiomyopathy characterized in a Thai clinical genetics service. | Trachoo O | PloS one | 2022 | PMID: 36166435 |
| MicroRNA expression profiles in familial hypertrophic cardiomyopathy with myosin-binding protein C3 (MYBPC3) gene mutations. | Lin LR | BMC cardiovascular disorders | 2022 | PMID: 35717150 |
| Diagnostic yield of genetic testing in a heterogeneous cohort of 1376 HCM patients. | Hathaway J | BMC cardiovascular disorders | 2021 | PMID: 33673806 |
| Spatial and Functional Distribution of MYBPC3 Pathogenic Variants and Clinical Outcomes in Patients With Hypertrophic Cardiomyopathy. | Helms AS | Circulation. Genomic and precision medicine | 2020 | PMID: 32841044 |
| Genetic Studies of Hypertrophic Cardiomyopathy in Singaporeans Identify Variants in TNNI3 and TNNT2 That Are Common in Chinese Patients. | Pua CJ | Circulation. Genomic and precision medicine | 2020 | PMID: 32815737 |
| Retrospective analysis of clinical phenotype and prognosis of hypertrophic cardiomyopathy complicated with hypertension. | Luo Q | Scientific reports | 2020 | PMID: 31941943 |
| Genotype and Lifetime Burden of Disease in Hypertrophic Cardiomyopathy: Insights from the Sarcomeric Human Cardiomyopathy Registry (SHaRe). | Ho CY | Circulation | 2018 | PMID: 30297972 |
| Genetic basis of channelopathies and cardiomyopathies in Hong Kong Chinese patients: a 10-year regional laboratory experience. | Mak CM | Hong Kong medical journal = Xianggang yi xue za zhi | 2018 | PMID: 29497013 |
| Multiple Gene Variants in Hypertrophic Cardiomyopathy in the Era of Next-Generation Sequencing. | Burns C | Circulation. Cardiovascular genetics | 2017 | PMID: 28790153 |
| Burden of Recurrent and Ancestral Mutations in Families With Hypertrophic Cardiomyopathy. | Ross SB | Circulation. Cardiovascular genetics | 2017 | PMID: 28615295 |
| Next-generation sequencing identifies pathogenic and modifier mutations in a consanguineous Chinese family with hypertrophic cardiomyopathy. | Zhang X | Medicine | 2017 | PMID: 28614222 |
| Identification of a novel hypertrophic cardiomyopathy-associated mutation using targeted next-generation sequencing. | Zhao Y | International journal of molecular medicine | 2017 | PMID: 28498465 |
| Nonfamilial Hypertrophic Cardiomyopathy: Prevalence, Natural History, and Clinical Implications. | Ingles J | Circulation. Cardiovascular genetics | 2017 | PMID: 28408708 |
| Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. | Walsh R | Genetics in medicine : official journal of the American College of Medical Genetics | 2017 | PMID: 27532257 |
| [P1208fs mutation in the cardiac myosin binding protein C is associated with hypertrophic cardiomyopathy in a Chinese pedigree]. | Li J | Zhonghua xin xue guan bing za zhi | 2016 | PMID: 27112610 |
| Evaluation of the Mayo Clinic Phenotype-Based Genotype Predictor Score in Patients with Clinically Diagnosed Hypertrophic Cardiomyopathy. | Murphy SL | Journal of cardiovascular translational research | 2016 | PMID: 26914223 |
| Screening Mutations of MYBPC3 in 114 Unrelated Patients with Hypertrophic Cardiomyopathy by Targeted Capture and Next-generation Sequencing. | Liu X | Scientific reports | 2015 | PMID: 26090888 |
| Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. | Richards S | Genetics in medicine : official journal of the American College of Medical Genetics | 2015 | PMID: 25741868 |
| Results of clinical genetic testing of 2,912 probands with hypertrophic cardiomyopathy: expanded panels offer limited additional sensitivity. | Alfares AA | Genetics in medicine : official journal of the American College of Medical Genetics | 2015 | PMID: 25611685 |
| Malignant effects of multiple rare variants in sarcomere genes on the prognosis of patients with hypertrophic cardiomyopathy. | Wang J | European journal of heart failure | 2014 | PMID: 25132132 |
| Mutation spectrum in a large cohort of unrelated Chinese patients with hypertrophic cardiomyopathy. | Liu W | The American journal of cardiology | 2013 | PMID: 23711808 |
| T1 measurements identify extracellular volume expansion in hypertrophic cardiomyopathy sarcomere mutation carriers with and without left ventricular hypertrophy. | Ho CY | Circulation. Cardiovascular imaging | 2013 | PMID: 23549607 |
| Multiple gene mutations, not the type of mutation, are the modifier of left ventricle hypertrophy in patients with hypertrophic cardiomyopathy. | Zou Y | Molecular biology reports | 2013 | PMID: 23283745 |
| [Link between cardiac myosin binding protein-C gene mutation of Pro1208fs and Gly507 Arg and hypertrophic cardiomyopathy in Chinese patients]. | Li M | Zhonghua xin xue guan bing za zhi | 2009 | PMID: 20128375 |
| Evidence from human myectomy samples that MYBPC3 mutations cause hypertrophic cardiomyopathy through haploinsufficiency. | Marston S | Circulation research | 2009 | PMID: 19574547 |
| click to load more citations click to collapse | ||||
Text-mined citations for rs397516029 ...
HelpRecord last updated Aug 04, 2026
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.
