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NM_001289808.2(CRYAB):c.116C>T (p.Pro39Leu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Uncertain significance(6)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Aug 5, 2021)
Last evaluated:
Oct 12, 2020
Accession:
VCV000178013.10
Variation ID:
178013
Description:
single nucleotide variant
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NM_001289808.2(CRYAB):c.116C>T (p.Pro39Leu)

Allele ID
178210
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q23.1
Genomic location
11: 111911609 (GRCh38) GRCh38 UCSC
11: 111782333 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.111911609G>A
NC_000011.9:g.111782333G>A
NG_009824.2:g.17114C>T
... more HGVS
Protein change
P39L
Other names
-
Canonical SPDI
NC_000011.10:111911608:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00011
The Genome Aggregation Database (gnomAD), exomes 0.00024
Trans-Omics for Precision Medicine (TOPMed) 0.00010
Exome Aggregation Consortium (ExAC) 0.00034
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00038
The Genome Aggregation Database (gnomAD) 0.00020
The Genome Aggregation Database (gnomAD) 0.00061
Links
ClinGen: CA181184
dbSNP: rs149787233
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Jul 1, 2016 RCV000154694.2
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000296232.2
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000335745.2
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000371984.2
Uncertain significance 1 criteria provided, single submitter Jan 21, 2019 RCV000617272.1
Uncertain significance 1 criteria provided, single submitter Oct 12, 2020 RCV000655018.4
Uncertain significance 1 criteria provided, single submitter Feb 14, 2020 RCV001550214.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CRYAB - - GRCh38
GRCh37
154 175

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Apr 12, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000204373.4
Submitted: (Mar 21, 2019)
Evidence details
Comment:
The Pro39Leu variant in CRYAB has not been reported in individuals with cardiomy opathy, but has been identified in 5/8594 European American chromosomes by the … (more)
Uncertain significance
(Jul 01, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000594225.1
Submitted: (Jul 05, 2017)
Evidence details
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Cataract 16, multiple types
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000367276.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Fatal infantile hypertonic myofibrillar myopathy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000367274.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Alpha-B crystallinopathy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000367275.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Jan 21, 2019)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000735832.3
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (1)
Comment:
The p.P39L variant (also known as c.116C>T), located in coding exon 1 of the CRYAB gene, results from a C to T substitution at nucleotide … (more)
Uncertain significance
(Oct 12, 2020)
criteria provided, single submitter
Method: clinical testing
Dilated cardiomyopathy 1II
Allele origin: germline
Invitae
Accession: SCV000776938.4
Submitted: (Jan 07, 2021)
Evidence details
Comment:
This sequence change replaces proline with leucine at codon 39 of the CRYAB protein (p.Pro39Leu). The proline residue is highly conserved and there is a … (more)
Uncertain significance
(Feb 14, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001770510.1
Submitted: (Aug 05, 2021)
Evidence details
Comment:
Previously reported in an individual with left ventricular non-compaction who also harbored variants in the LMNA and MYLK2 genes (Miszalski-Jamka et al., 2017); In silico … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Novel Genetic Triggers and Genotype-Phenotype Correlations in Patients With Left Ventricular Noncompaction. Miszalski-Jamka K Circulation. Cardiovascular genetics 2017 PMID: 28798025

Text-mined citations for rs149787233...

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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 Nov 27, 2021