NM_152641.4(ARID2):c.4640_4659del (p.Ala1547fs) AND Coffin-Siris syndrome 6

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 31, 2020
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:: RCV001198606.2

Allele description [Variation Report for NM_152641.4(ARID2):c.4640_4659del (p.Ala1547fs)]

NM_152641.4(ARID2):c.4640_4659del (p.Ala1547fs)

Gene:

ARID2:AT-rich interaction domain 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12q12

Genomic location:

Preferred name:

NM_152641.4(ARID2):c.4640_4659del (p.Ala1547fs)

HGVS:

NC_000012.12:g.45852763_45852782del
NG_052800.1:g.128099_128118del
NM_001347839.2:c.4640_4659del
NM_152641.4:c.4640_4659delMANE SELECT
NP_001334768.1:p.Ala1547fs
NP_689854.2:p.Ala1547fs
NC_000012.11:g.46246546_46246565del
NM_152641.2:c.4640_4659delCTGGCTGCAGCGCAACAATG

Protein change:

A1547fs

Links:

dbSNP: rs1943579551

NCBI 1000 Genomes Browser:

rs1943579551

Molecular consequence:

NM_001347839.2:c.4640_4659del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_152641.4:c.4640_4659del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Coffin-Siris syndrome 6
Identifiers:: MONDO: MONDO:0033492; MedGen: C4540499; OMIM: 617808

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001369598	Centre for Mendelian Genomics, University Medical Centre Ljubljana	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 31, 2020)	unknown	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

SCV001369598

Centre for Mendelian Genomics, University Medical Centre Ljubljana

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 31, 2020)

unknown

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	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001369598.2

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

Description

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS2-MOD,PM2.

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

Last Updated: Dec 17, 2022

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