NM_016239.4(MYO15A):c.6403G>T (p.Val2135Leu) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 5, 2022
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:: RCV003114367.4

Allele description [Variation Report for NM_016239.4(MYO15A):c.6403G>T (p.Val2135Leu)]

NM_016239.4(MYO15A):c.6403G>T (p.Val2135Leu)

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.6403G>T (p.Val2135Leu)

HGVS:

NC_000017.11:g.18146001G>T
NG_011634.2:g.42296G>T
NM_016239.4:c.6403G>TMANE SELECT
NP_057323.3:p.Val2135Leu
NC_000017.10:g.18049315G>T
NG_011634.1:g.42296G>T
NM_016239.3:c.6403G>T

Protein change:

V2135L

Links:

dbSNP: rs374716848

NCBI 1000 Genomes Browser:

rs374716848

Molecular consequence:

NM_016239.4:c.6403G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Rhodobacter sphaeroides strain RSF3 16S ribosomal RNA gene, partial sequence
Rhodobacter sphaeroides strain RSF3 16S ribosomal RNA gene, partial sequence
gi|557836197|gb|KF606893.1|

Nucleotide
Cereibacter sphaeroides strain PNSBFraternidad_1 16S ribosomal RNA gene, partial...
Cereibacter sphaeroides strain PNSBFraternidad_1 16S ribosomal RNA gene, partial sequence
gi|1018684906|gb|KU992651.1|

Nucleotide
Garymunida squamosa voucher NMV<AUS>:J57243 cytochrome oxidase subunit I (COI) g...
Garymunida squamosa voucher NMV<AUS>:J57243 cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
gi|1865527867|gb|MK848030.1|

Nucleotide
cytochrome c oxidase subunit I, partial (mitochondrion) [Celastrina lavendularis...
cytochrome c oxidase subunit I, partial (mitochondrion) [Celastrina lavendularis limbata]
gi|2644499093|gb|WRI52353.1|

Protein
4930488B01Rik RIKEN cDNA 4930488B01 gene [Mus musculus]
4930488B01Rik RIKEN cDNA 4930488B01 gene [Mus musculus]
Gene ID:75036

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003789433	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 5, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 31997689, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003789433

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 5, 2022)

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

Investigation of MYO15A and MYO7A Mutations in Iranian Patients with Nonsyndromic Hearing Loss.

Farjami M, Fathi M, Ghasemi MM, Rajati M, Eslahi A, Alimardani M, Mojarrad M.

Fetal Pediatr Pathol. 2021 Apr;40(2):121-130. doi: 10.1080/15513815.2019.1686790. Epub 2020 Jan 30.

PubMed [citation]

PMID:: 31997689

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, SCV003789433.2

#	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 valine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 2135 of the MYO15A protein (p.Val2135Leu). This variant is present in population databases (rs374716848, gnomAD 0.009%). This missense change has been observed in individual(s) with MYO15A-related conditions (PMID: 31997689). ClinVar contains an entry for this variant (Variation ID: 218732). 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 not expected to disrupt MYO15A protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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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