VCV000417019.20 - ClinVar

NM_032578.4(MYPN):c.2409C>A (p.Ser803Arg)

Germline

Classification

criteria provided, conflicting classifications. Learn more about how ClinVar calculates review status.

Conflicting classifications of pathogenicity
Uncertain significance (1); Likely benign (3)

4 out of 4 submissions contributed to this classification

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.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_032578.4(MYPN):c.2409C>A (p.Ser803Arg)

Variation ID: 417019 Accession: VCV000417019.20

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 10q21.3 10: 68174501 (GRCh38) [ NCBI UCSC ] 10: 69934258 (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	Apr 14, 2018	Feb 15, 2026	Oct 2, 2025

HGVS

Nucleotide	Protein	Molecular consequence
NM_032578.4:c.2409C>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_115967.2:p.Ser803Arg	missense
NM_001256267.2:c.2409C>A	NP_001243196.1:p.Ser803Arg	missense
NM_001256268.2:c.1527C>A	NP_001243197.1:p.Ser509Arg	missense
NR_045662.4:n.1946C>A		non-coding transcript variant
NR_045663.4:n.2622C>A		non-coding transcript variant
NC_000010.11:g.68174501C>A
NC_000010.10:g.69934258C>A
NG_032118.1:g.73385C>A
LRG_410:g.73385C>A
LRG_410t1:c.2409C>A	LRG_410p1:p.Ser803Arg

... more HGVS ... less HGVS

Protein change

S803R, S509R

Other names

p.Ser803Arg

Canonical SPDI

NC_000010.11:68174500:C:A

Global minor allele frequency (GMAF) Help The 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.

0.47145 (G)

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA5522783 dbSNP: rs3814182 VarSome

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
Gene	OMIM	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.
MYPN		-	-	GRCh38 GRCh37	1942	1993

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.
Dilated cardiomyopathy 1KK	Likely benign (1)	criteria provided, single submitter	Oct 2, 2025	RCV000463865.13
Cardiovascular phenotype	Likely benign (1)	criteria provided, single submitter	Jul 5, 2024	RCV000619222.4
not provided	Conflicting classifications of pathogenicity (2)	criteria provided, conflicting classifications	Jan 27, 2023	RCV001584192.6

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.
Likely benign (Dec 08, 2020) C Contributing to aggregate classification	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	not provided	GeneDx Accession: SCV001814076.1 First in ClinVar: Sep 08, 2021 Last updated: Sep 08, 2021	Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: yes Observation 1 Collection method: clinical testing Allele origin: germline Affected status: yes

Uncertain significance (Jan 27, 2023) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015)	not provided	Mayo Clinic Laboratories, Mayo Clinic Accession: SCV004225257.1 First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024	Comment: show BP4 (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown more Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Number of individuals with the variant: 1

Likely benign (Jul 05, 2024) C Contributing to aggregate classification	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Cardiovascular phenotype	Ambry Genetics Accession: SCV000735870.6 First in ClinVar: Apr 14, 2018 Last updated: Jan 13, 2025	Publications: PubMed (3) PubMed: 18006477‚ 22286171‚ 23861362 Comment: show This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (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

Likely benign (Oct 02, 2025) C Contributing to aggregate classification	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Dilated cardiomyopathy 1KK	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV000563298.11 First in ClinVar: Apr 17, 2017 Last updated: Feb 15, 2026	Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Comment:

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Interpreting secondary cardiac disease variants in an exome cohort.	Ng D	Circulation. Cardiovascular genetics	2013	PMID: 23861362
Molecular basis for clinical heterogeneity in inherited cardiomyopathies due to myopalladin mutations.	Purevjav E	Human molecular genetics	2012	PMID: 22286171
Mutations in the Z-band protein myopalladin gene and idiopathic dilated cardiomyopathy.	Duboscq-Bidot L	Cardiovascular research	2008	PMID: 18006477

Text-mined citations for rs3814182 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Feb 15, 2026