NM_016239.4(MYO15A):c.4441T>C (p.Ser1481Pro) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 6, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003558853.1

Allele description [Variation Report for NM_016239.4(MYO15A):c.4441T>C (p.Ser1481Pro)]

NM_016239.4(MYO15A):c.4441T>C (p.Ser1481Pro)

Gene:

MYO15A:myosin XVA [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p11.2

Genomic location:

Preferred name:

NM_016239.4(MYO15A):c.4441T>C (p.Ser1481Pro)

HGVS:

NC_000017.11:g.18133345T>C
NG_011634.2:g.29640T>C
NM_016239.4:c.4441T>CMANE SELECT
NP_057323.3:p.Ser1481Pro
NC_000017.10:g.18036659T>C

Protein change:

S1481P

Links:

dbSNP: rs758896141

NCBI 1000 Genomes Browser:

rs758896141

Molecular consequence:

NM_016239.4:c.4441T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004298144	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 6, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 20642360, 30953472, 35346193, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004298144

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 6, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Recurrent and private MYO15A mutations are associated with deafness in the Turkish population.

Cengiz FB, Duman D, Sirmaci A, Tokgöz-Yilmaz S, Erbek S, Oztürkmen-Akay H, Incesulu A, Edwards YJ, Ozdag H, Liu XZ, Tekin M.

Genet Test Mol Biomarkers. 2010 Aug;14(4):543-50. doi: 10.1089/gtmb.2010.0039.

PubMed [citation]

PMID:: 20642360

Genotype-phenotype correlation analysis of MYO15A variants in autosomal recessive non-syndromic hearing loss.

Zhang J, Guan J, Wang H, Yin L, Wang D, Zhao L, Zhou H, Wang Q.

BMC Med Genet. 2019 Apr 5;20(1):60. doi: 10.1186/s12881-019-0790-2.

PubMed [citation]

PMID:: 30953472
PMCID:: PMC6451310

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV004298144.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MYO15A protein function. ClinVar contains an entry for this variant (Variation ID: 1301927). This missense change has been observed in individuals with deafness (PMID: 20642360, 30953472, 35346193). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs758896141, gnomAD 0.006%). This sequence change replaces serine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 1481 of the MYO15A protein (p.Ser1481Pro).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 20, 2024

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