NM_015570.4(AUTS2):c.1969G>A (p.Ala657Thr) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 9, 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:: RCV003702887.2

Allele description [Variation Report for NM_015570.4(AUTS2):c.1969G>A (p.Ala657Thr)]

NM_015570.4(AUTS2):c.1969G>A (p.Ala657Thr)

Gene:

AUTS2:activator of transcription and developmental regulator AUTS2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q11.22

Genomic location:

Preferred name:

NM_015570.4(AUTS2):c.1969G>A (p.Ala657Thr)

HGVS:

NC_000007.14:g.70777139G>A
NG_034133.1:g.1183221G>A
NM_001127231.3:c.1897G>A
NM_015570.4:c.1969G>AMANE SELECT
NP_001120703.1:p.Ala633Thr
NP_056385.1:p.Ala657Thr
NC_000007.13:g.70242125G>A

Protein change:

A633T

Molecular consequence:

NM_001127231.3:c.1897G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015570.4:c.1969G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Selenohomolysine AND 1[s_discriminator] (0)
dbGaP
isochorismatase domain-containing protein 2 isoform X3 [Rattus norvegicus]
isochorismatase domain-containing protein 2 isoform X3 [Rattus norvegicus]
gi|2678868163|ref|XP_063122337.1|

Protein
Homo sapiens chloride voltage-gated channel 7 (CLCN7), transcript variant 2, mRN...
Homo sapiens chloride voltage-gated channel 7 (CLCN7), transcript variant 2, mRNA
gi|1890270818|ref|NM_001114331.3|

Nucleotide
Crenicichla punctata isolate DNA9 cytochrome b gene, partial cds; mitochondrial
Crenicichla punctata isolate DNA9 cytochrome b gene, partial cds; mitochondrial
gi|343949890|gb|JF519956.1|

Nucleotide
Prototrachelocerca fasciolata isolate YY2012041802 small subunit ribosomal RNA g...
Prototrachelocerca fasciolata isolate YY2012041802 small subunit ribosomal RNA gene, partial sequence
gi|675153698|gb|KJ609035.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004470255	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 9, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004470255

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 9, 2023)

germline

clinical testing

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

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

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, SCV004470255.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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. 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 AUTS2 protein function. This variant has not been reported in the literature in individuals affected with AUTS2-related conditions. This variant is present in population databases (rs750187638, gnomAD 0.002%). This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 657 of the AUTS2 protein (p.Ala657Thr).

#	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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