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NM_006015.6(ARID1A):c.31_56del (p.Ser11fs) AND Coffin-Siris syndrome 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 15, 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:
RCV003314556.1

Allele description [Variation Report for NM_006015.6(ARID1A):c.31_56del (p.Ser11fs)]

NM_006015.6(ARID1A):c.31_56del (p.Ser11fs)

Gene:
ARID1A:AT-rich interaction domain 1A [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1p36.11
Genomic location:
Preferred name:
NM_006015.6(ARID1A):c.31_56del (p.Ser11fs)
HGVS:
  • NC_000001.11:g.26696434_26696459del
  • NG_029965.1:g.5404_5429del
  • NM_006015.6:c.31_56delMANE SELECT
  • NM_139135.4:c.31_56del
  • NP_006006.3:p.Ser11fs
  • NP_624361.1:p.Ser11fs
  • LRG_875t1:c.31_56del
  • LRG_875t1:c.31_56del26
  • LRG_875:g.5404_5429del
  • NC_000001.10:g.27022925_27022950del
  • NM_006015.4:c.31_56del26
  • NM_006015.4:c.31_56delAGCAGCCTGGGCAACCCGCCGCCGCC
Note:
NCBI staff reviewed the sequence information reported in PubMed 22426308 Supplementary Fig. 4 to determine the location of this allele on the current reference sequence.
Protein change:
S11fs
Links:
OMIM: 603024.0001; dbSNP: rs797045262
NCBI 1000 Genomes Browser:
rs797045262
Molecular consequence:
  • NM_006015.6:c.31_56del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_139135.4:c.31_56del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Coffin-Siris syndrome 1 (CSS1)
Synonyms:
Mental retardation, autosomal dominant 12
Identifiers:
MONDO: MONDO:0007617; MedGen: C3281201; Orphanet: 1465; OMIM: 135900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004014664Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSLVariantClassificationCriteria RUGD 01 April 2020)		Pathogenic
(May 15, 2023) 		unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

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Summary from all submissions

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

Citations

PubMed

Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome.

Tsurusaki Y, Okamoto N, Ohashi H, Kosho T, Imai Y, Hibi-Ko Y, Kaname T, Naritomi K, Kawame H, Wakui K, Fukushima Y, Homma T, Kato M, Hiraki Y, Yamagata T, Yano S, Mizuno S, Sakazume S, Ishii T, Nagai T, Shiina M, Ogata K, et al.

Nat Genet. 2012 Mar 18;44(4):376-8. doi: 10.1038/ng.2219.

PubMed [citation]
PMID:
22426308

Genotype-phenotype correlation of Coffin-Siris syndrome caused by mutations in SMARCB1, SMARCA4, SMARCE1, and ARID1A.

Kosho T, Okamoto N; Coffin-Siris Syndrome International Collaborators..

Am J Med Genet C Semin Med Genet. 2014 Sep;166C(3):262-75. doi: 10.1002/ajmg.c.31407. Epub 2014 Aug 28.

PubMed [citation]
PMID:
25168959

Details of each submission

From Illumina Laboratory Services, Illumina, SCV004014664.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

The ARID1A c.31_56del (p.Ser11AlafsTer91) variant causes a shift in the protein reading frame that is predicted to result in premature termination of the protein. Loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay is expected. This variant has been reported in one individual with Coffin-Siris syndrome, in whom parental samples were unavailable to confirm the de novo status of the variant (PMID: 22426308; 25168959). The p.Ser11AlafsTer91 variant is not observed in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. This variant was identified in a de novo state. Based on the available evidence, the c.31_56del (p.Ser11AlafsTer91) variant is classified as pathogenic for Coffin-Siris syndrome.

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

Last Updated: Sep 8, 2024