NM_001614.5(ACTG1):c.520G>A (p.Ala174Thr) AND Autosomal dominant nonsyndromic hearing loss 20

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 19, 2020
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:: RCV002272976.3

Allele description [Variation Report for NM_001614.5(ACTG1):c.520G>A (p.Ala174Thr)]

NM_001614.5(ACTG1):c.520G>A (p.Ala174Thr)

Gene:

ACTG1:actin gamma 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q25.3

Genomic location:

Preferred name:

NM_001614.5(ACTG1):c.520G>A (p.Ala174Thr)

HGVS:

NC_000017.11:g.81511470C>T
NG_011433.1:g.6332G>A
NM_001199954.3:c.520G>A
NM_001614.5:c.520G>AMANE SELECT
NP_001186883.1:p.Ala174Thr
NP_001605.1:p.Ala174Thr
NC_000017.10:g.79478496C>T
NM_001199954.2:c.520G>A
NR_037688.3:n.592G>A

Protein change:

A174T

Links:

dbSNP: rs587780274

NCBI 1000 Genomes Browser:

rs587780274

Molecular consequence:

NM_001199954.3:c.520G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001614.5:c.520G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_037688.3:n.592G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Autosomal dominant nonsyndromic hearing loss 20
Synonyms:: Deafness, autosomal dominant 20
Identifiers:: MONDO: MONDO:0011480; MedGen: C1858172; Orphanet: 90635; OMIM: 604717

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002557482	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 19, 2020)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 29907799, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002557482

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 19, 2020)

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

Utility and limitations of exome sequencing as a genetic diagnostic tool for children with hearing loss.

Sheppard S, Biswas S, Li MH, Jayaraman V, Slack I, Romasko EJ, Sasson A, Brunton J, Rajagopalan R, Sarmady M, Abrudan JL, Jairam S, DeChene ET, Ying X, Choi J, Wilkens A, Raible SE, Scarano MI, Santani A, Pennington JW, Luo M, Conlin LK, et al.

Genet Med. 2018 Dec;20(12):1663-1676. doi: 10.1038/s41436-018-0004-x. Epub 2018 Jun 15.

PubMed [citation]

PMID:: 29907799
PMCID:: PMC6295269

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002557482.2

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

Description

Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as 3B-VUS. Following criteria are met: 0101 - Gain-of-function is a known mechanism of disease for this gene. (N) 0107 - This gene is known to be associated with autosomal dominant disease. (N) 0200 - Variant is predicted to result in a missense amino acid change from alanine to threonine (exon 4). (N) 0251 - Variant is heterozygous. (N) 0301 - Variant is absent from gnomAD. (P) 0309 - An alternative amino acid change at the same position has been observed in gnomAD v2 (1 heterozygote, 0 homozygotes). (N) 0502 - Missense variant with conflicting in silico predictions and/or uninformative conservation. (N) 0603 - Missense variant in a region that is highly intolerant to missense variation (high constraint region) (actin domain; PDB). (P) 0705 - No comparable variants have previous evidence for pathogenicity. Alternative changes at the same residue (p.Ala174Ser, p.Ala174Gly) have been reported as VUS (ClinVar, deafnessvariationdatabase, LOVD, PMID: 29907799). (N) 0807 - Variant has not previously been reported in a clinical context. (N) 0905 - No segregation evidence has been identified for this variant. (N) 1007 - No published functional evidence has been identified for this variant. (N) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign

#	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: Jul 23, 2024

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