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NM_001374828.1(ARID1B):c.2762-1G>C AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 17, 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:
RCV003688218.2

Allele description [Variation Report for NM_001374828.1(ARID1B):c.2762-1G>C]

NM_001374828.1(ARID1B):c.2762-1G>C

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.2762-1G>C
HGVS:
  • NC_000006.12:g.157148623G>C
  • NG_066624.1:g.377598G>C
  • NM_001363725.2:c.263-1G>C
  • NM_001371656.1:c.2801-1G>C
  • NM_001374820.1:c.2801-1G>C
  • NM_001374828.1:c.2762-1G>CMANE SELECT
  • NM_017519.3:c.2762-1G>C
  • NC_000006.11:g.157469757G>C
Molecular consequence:
  • NM_001363725.2:c.263-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001371656.1:c.2801-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001374820.1:c.2801-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001374828.1:c.2762-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_017519.3:c.2762-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV004449916Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Aug 17, 2023) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Genetic abnormalities in a large cohort of Coffin-Siris syndrome patients.

Sekiguchi F, Tsurusaki Y, Okamoto N, Teik KW, Mizuno S, Suzumura H, Isidor B, Ong WP, Haniffa M, White SM, Matsuo M, Saito K, Phadke S, Kosho T, Yap P, Goyal M, Clarke LA, Sachdev R, McGillivray G, Leventer RJ, Patel C, Yamagata T, et al.

J Hum Genet. 2019 Dec;64(12):1173-1186. doi: 10.1038/s10038-019-0667-4. Epub 2019 Sep 17.

PubMed [citation]
PMID:
31530938

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004449916.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Disruption of this splice site has been observed in individual(s) with clinical features of Coffin-Siris syndrome (PMID: 31530938). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 8 of the ARID1B gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ARID1B are known to be pathogenic (PMID: 25674384, 30349098). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Sep 29, 2024