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NM_001374828.1(ARID1B):c.5126C>T (p.Thr1709Met) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Jan 1, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV002944202.13

Allele description [Variation Report for NM_001374828.1(ARID1B):c.5126C>T (p.Thr1709Met)]

NM_001374828.1(ARID1B):c.5126C>T (p.Thr1709Met)

Gene:
ARID1B:AT-rich interaction domain 1B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6q25.3
Genomic location:
Preferred name:
NM_001374828.1(ARID1B):c.5126C>T (p.Thr1709Met)
HGVS:
  • NC_000006.12:g.157201351C>T
  • NG_066624.1:g.430326C>T
  • NM_001346813.1:c.4877C>T
  • NM_001363725.2:c.2627C>T
  • NM_001371656.1:c.5006C>T
  • NM_001374820.1:c.5006C>T
  • NM_001374828.1:c.5126C>TMANE SELECT
  • NM_017519.3:c.4967C>T
  • NM_020732.3:c.4757C>T
  • NM_175863.2:c.4544C>T
  • NP_001333742.1:p.Thr1626Met
  • NP_001350654.1:p.Thr876Met
  • NP_001358585.1:p.Thr1669Met
  • NP_001361749.1:p.Thr1669Met
  • NP_001361757.1:p.Thr1709Met
  • NP_059989.3:p.Thr1656Met
  • NP_065783.3:p.Thr1586Met
  • NP_787059.2:p.Thr1515Met
  • NC_000006.11:g.157522485C>T
Protein change:
T1515M
Molecular consequence:
  • NM_001346813.1:c.4877C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363725.2:c.2627C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371656.1:c.5006C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374820.1:c.5006C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374828.1:c.5126C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_017519.3:c.4967C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020732.3:c.4757C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_175863.2:c.4544C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
3

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003286371Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 11, 2023) 		germlineclinical testing

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

SCV004156302CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)		Likely benign
(Jan 1, 2024) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes3not providednot providednot providednot providedclinical testing
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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003286371.2

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

Description

This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 1586 of the ARID1B protein (p.Thr1586Met). This variant is present in population databases (rs777745107, gnomAD 0.01%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with ARID1B-related conditions. ClinVar contains an entry for this variant (Variation ID: 2073985). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on ARID1B protein function. 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.

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

From CeGaT Center for Human Genetics Tuebingen, SCV004156302.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testingnot provided

Description

ARID1B: BP4, BS2

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided3not providednot providednot provided

Last Updated: Oct 8, 2024