NM_001374828.1(ARID1B):c.6199C>T (p.Arg2067Ter) AND Coffin-Siris syndrome 1

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jul 15, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000496177.4

Allele description [Variation Report for NM_001374828.1(ARID1B):c.6199C>T (p.Arg2067Ter)]

NM_001374828.1(ARID1B):c.6199C>T (p.Arg2067Ter)

Gene:

ARID1B:AT-rich interaction domain 1B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q25.3

Genomic location:

Preferred name:

NM_001374828.1(ARID1B):c.6199C>T (p.Arg2067Ter)

HGVS:

NC_000006.12:g.157206971C>T
NG_066624.1:g.435946C>T
NM_001363725.2:c.3700C>T
NM_001371656.1:c.6079C>T
NM_001374820.1:c.6079C>T
NM_001374828.1:c.6199C>TMANE SELECT
NM_017519.3:c.6040C>T
NM_020732.3:c.5830C>T
NP_001350654.1:p.Arg1234Ter
NP_001358585.1:p.Arg2027Ter
NP_001361749.1:p.Arg2027Ter
NP_001361757.1:p.Arg2067Ter
NP_059989.3:p.Arg2014Ter
NP_065783.3:p.Arg1944Ter
NC_000006.11:g.157528105C>T
NM_001374828.1:c.6199C>T

Protein change:

R1234*

Links:

dbSNP: rs1028186690

NCBI 1000 Genomes Browser:

rs1028186690

Molecular consequence:

NM_001363725.2:c.3700C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001371656.1:c.6079C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001374820.1:c.6079C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001374828.1:c.6199C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_017519.3:c.6040C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_020732.3:c.5830C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

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
SCV000586772	Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement, Assistance Publique Hopitaux de Paris	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 6, 2017)	paternal	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 28708303
SCV002054295	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 15, 2021)	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

SCV000586772

Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement, Assistance Publique Hopitaux de Paris

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 6, 2017)

paternal

clinical testing

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

SCV002054295

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 15, 2021)

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	paternal	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Using medical exome sequencing to identify the causes of neurodevelopmental disorders: Experience of 2 clinical units and 216 patients.

Chérot E, Keren B, Dubourg C, Carré W, Fradin M, Lavillaureix A, Afenjar A, Burglen L, Whalen S, Charles P, Marey I, Heide S, Jacquette A, Heron D, Doummar D, Rodriguez D, Billette de Villemeur T, Moutard ML, Guët A, Xavier J, Périsse D, Cohen D, et al.

Clin Genet. 2018 Mar;93(3):567-576. doi: 10.1111/cge.13102. Epub 2017 Oct 4.

PubMed [citation]

PMID:: 28708303

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 Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement, Assistance Publique Hopitaux de Paris, SCV000586772.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)

Description

hypotonia; Intellectual disability, moderate; dysmorphism

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

From Genome-Nilou Lab, SCV002054295.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

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