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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004014664	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSLVariantClassificationCriteria RUGD 01 April 2020)	Pathogenic (May 15, 2023)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22426308, 25168959 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004014664

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSLVariantClassificationCriteria RUGD 01 April 2020)

Pathogenic
(May 15, 2023)

unknown

clinical testing

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

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jul 22, 2023

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