VCV003383946.1 - ClinVar

NM_016239.4(MYO15A):c.8158G>A (p.Asp2720Asn)

Germline

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.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_016239.4(MYO15A):c.8158G>A (p.Asp2720Asn)

Variation ID: 3383946 Accession: VCV003383946.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 17p11.2 17: 18154689 (GRCh38) [ NCBI UCSC ] 17: 18058003 (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	Dec 7, 2024	Dec 7, 2024	Jan 6, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_016239.4:c.8158G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_057323.3:p.Asp2720Asn	missense
NC_000017.11:g.18154689G>A
NC_000017.10:g.18058003G>A
NG_011634.2:g.50984G>A

Protein change

D2720N

Other names

Canonical SPDI

NC_000017.11:18154688:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

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.

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

Links

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.
MYO15A		-	-	GRCh38 GRCh37	-	-

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.
Autosomal recessive nonsyndromic hearing loss 3	Pathogenic (1)	no assertion criteria provided	Jan 6, 2024	RCV004798695.1

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.	More information 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 (Jan 06, 2024)	no assertion criteria provided Method: research	Autosomal recessive nonsyndromic hearing loss 3 (Autosomal recessive inheritance) Affected status: yes Allele origin: unknown	Wonkam Laboratory, Johns Hopkins University Accession: SCV005420297.1 First in ClinVar: Dec 07, 2024 Last updated: Dec 07, 2024	Publications: PubMed (2) PubMed: 30953472‚ 31992338 Comment: The variant NM_016239.3 c.8158G is reported in reputable source (Pubmed) recently reports variant as pathogenic (PP5), located in a mutational hot spot and/or critical and … (more) The variant NM_016239.3 c.8158G is reported in reputable source (Pubmed) recently reports variant as pathogenic (PP5), located in a mutational hot spot and/or critical and well-established functional domain (PM1), Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium (PM2), Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease (PP1), Multiple lines of computational evidence support a deleterious effect on the gene or gene product (PP3), Patient's phenotype or family history is highly specific for a disease with a single genetic etiology (PP4) (less) Number of individuals with the variant: 2 Clinical Features: Nonsyndromic profound hearing loss (present) Family history: yes Secondary finding: no

Comment:

The variant NM_016239.3 c.8158G is reported in reputable source (Pubmed) recently reports variant as pathogenic (PP5), located in a mutational hot spot and/or critical and well-established functional domain (PM1), Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium (PM2), Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease (PP1), Multiple lines of computational evidence support a deleterious effect on the gene or gene product (PP3), Patient's phenotype or family history is highly specific for a disease with a single genetic etiology (PP4)

Germline Functional Evidence

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.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Molecular epidemiology of Chinese Han deaf patients with bi-allelic and mono-allelic GJB2 mutations.	Yu X	Orphanet journal of rare diseases	2020	PMID: 31992338
Genotype-phenotype correlation analysis of MYO15A variants in autosomal recessive non-syndromic hearing loss.	Zhang J	BMC medical genetics	2019	PMID: 30953472

Text-mined citations for this variant ...

Record last updated Dec 07, 2024

ClinVar Genomic variation as it relates to human health

NM_016239.4(MYO15A):c.8158G>A (p.Asp2720Asn)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...