NM_006015.6(ARID1A):c.31_56del (p.Ser11fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 22, 2022
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:: RCV000480869.5

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)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000566684	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 22, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000566684

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Mar 22, 2022)

germline

clinical testing

Citation Link

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

Details of each submission

From GeneDx, SCV000566684.6

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

Description

Identified in a patient with Coffin-Siris syndrome in the published literature (Tsurusaki et al., 2012; Kosho et al., 2014); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25168959, 24090879, 27082517, 22426308)

#	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: Sep 8, 2024

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