NM_000260.4(MYO7A):c.1945C>T (p.Arg649Trp) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 3, 2024
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:: RCV001301731.7

Allele description [Variation Report for NM_000260.4(MYO7A):c.1945C>T (p.Arg649Trp)]

NM_000260.4(MYO7A):c.1945C>T (p.Arg649Trp)

Gene:

MYO7A:myosin VIIA [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.5

Genomic location:

Preferred name:

NM_000260.4(MYO7A):c.1945C>T (p.Arg649Trp)

HGVS:

NC_000011.10:g.77174765C>T
NG_009086.2:g.51520C>T
NM_000260.4:c.1945C>TMANE SELECT
NM_001127180.2:c.1945C>T
NM_001369365.1:c.1912C>T
NP_000251.3:p.Arg649Trp
NP_001120652.1:p.Arg649Trp
NP_001356294.1:p.Arg638Trp
LRG_1420t1:c.1945C>T
LRG_1420:g.51520C>T
LRG_1420p1:p.Arg649Trp
NC_000011.9:g.76885811C>T
NG_009086.1:g.51502C>T
NM_000260.3:c.1945C>T

Protein change:

R638W

Links:

dbSNP: rs782503314

NCBI 1000 Genomes Browser:

rs782503314

Molecular consequence:

NM_000260.4:c.1945C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127180.2:c.1945C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369365.1:c.1912C>T - 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
SCV001490909	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 3, 2024)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 34416374, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001490909

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 3, 2024)

germline

clinical testing

PubMed (2)
[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

Family trio-based sequencing in 404 sporadic bilateral hearing loss patients discovers recessive and De novo genetic variants in multiple ways.

Guan J, Li J, Chen G, Shi T, Lan L, Wu X, Zhao C, Wang D, Wang H, Wang Q.

Eur J Med Genet. 2021 Oct;64(10):104311. doi: 10.1016/j.ejmg.2021.104311. Epub 2021 Aug 17.

PubMed [citation]

PMID:: 34416374

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001490909.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 649 of the MYO7A protein (p.Arg649Trp). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with autosomal recessive deafness (PMID: 34416374). ClinVar contains an entry for this variant (Variation ID: 229000). 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) performed at Invitae indicates that this missense variant is expected to disrupt MYO7A protein function with a positive predictive value of 95%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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