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NM_005982.4(SIX1):c.775G>T (p.Gly259Cys) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 14, 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:
RCV003075541.2

Allele description [Variation Report for NM_005982.4(SIX1):c.775G>T (p.Gly259Cys)]

NM_005982.4(SIX1):c.775G>T (p.Gly259Cys)

Gene:
SIX1:SIX homeobox 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q23.1
Genomic location:
Preferred name:
NM_005982.4(SIX1):c.775G>T (p.Gly259Cys)
HGVS:
  • NC_000014.9:g.60646363C>A
  • NG_008231.1:g.8075G>T
  • NM_005982.4:c.775G>TMANE SELECT
  • NP_005973.1:p.Gly259Cys
  • NC_000014.8:g.61113081C>A
Protein change:
G259C
Molecular consequence:
  • NM_005982.4:c.775G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Branchiootic syndrome 3 (BOS3)
Synonyms:
BO SYNDROME 3
Identifiers:
MONDO: MONDO:0012025; MedGen: C1842124; OMIM: 608389
Name:
Autosomal dominant nonsyndromic hearing loss 23
Synonyms:
Deafness, autosomal dominant 23
Identifiers:
MONDO: MONDO:0011519; MedGen: C1854594; Orphanet: 90635; OMIM: 605192

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003469718Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jun 14, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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 Invitae, SCV003469718.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with SIX1-related conditions. This variant is present in population databases (rs779084301, gnomAD 0.006%). This sequence change replaces glycine, which is neutral and non-polar, with cysteine, which is neutral and slightly polar, at codon 259 of the SIX1 protein (p.Gly259Cys).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024