NM_006015.6(ARID1A):c.31_56del (p.Ser11fs) AND Intellectual disability, autosomal dominant 14

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jun 2, 2015
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:: RCV000023227.9

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:: Intellectual disability, autosomal dominant 14 (CSS2)
Synonyms:: COFFIN-SIRIS SYNDROME 2
Identifiers:: MONDO: MONDO:0013819; MedGen: C3553247; Orphanet: 1465; OMIM: 614607

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000044518	OMIM	no assertion criteria provided	Pathogenic (Mar 18, 2012)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000246490	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 2, 2015)	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

SCV000044518

OMIM

no assertion criteria provided

Pathogenic
(Mar 18, 2012)

germline

literature only

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

SCV000246490

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 2, 2015)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From OMIM, SCV000044518.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In Patient 3 with Coffin-Siris syndrome (CSS2; 614607), Tsurusaki et al. (2012) detected a heterozygous 26-bp deletion (31_56del) in the ARID1A gene, resulting in frameshift and premature termination 91 amino acids downstream (Ser11AlafsTer91). The patient presented with hepatoblastoma as well as multiple congenital anomalies. This mutation was not identified in 330 control chromosomes or in the dbSNP (build 132), 1000 Genomes Project, or Exome Sequencing Project databases. The parents were unavailable for testing.

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

From Genetic Services Laboratory, University of Chicago, SCV000246490.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

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

Last Updated: Jul 22, 2023

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