NM_001374828.1(ARID1B):c.6145C>T (p.Arg2049Ter) AND Coffin-Siris syndrome 1

Germline classification:: Pathogenic (6 submissions)
Last evaluated:: Sep 27, 2022
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:: RCV000625417.12

Allele description [Variation Report for NM_001374828.1(ARID1B):c.6145C>T (p.Arg2049Ter)]

NM_001374828.1(ARID1B):c.6145C>T (p.Arg2049Ter)

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.6145C>T (p.Arg2049Ter)

HGVS:

NC_000006.12:g.157206917C>T
NG_066624.1:g.435892C>T
NM_001363725.2:c.3646C>T
NM_001371656.1:c.6025C>T
NM_001374820.1:c.6025C>T
NM_001374828.1:c.6145C>TMANE SELECT
NM_017519.3:c.5986C>T
NM_020732.3:c.5776C>T
NP_001350654.1:p.Arg1216Ter
NP_001358585.1:p.Arg2009Ter
NP_001361749.1:p.Arg2009Ter
NP_001361757.1:p.Arg2049Ter
NP_059989.2:p.Arg1913Ter
NP_059989.3:p.Arg1996Ter
NP_065783.3:p.Arg1926Ter
NC_000006.11:g.157528051C>T
NM_001374828.1:c.6145C>T
NM_017519.2:c.5737C>T

Protein change:

R1216*

Links:

dbSNP: rs1554237658

NCBI 1000 Genomes Browser:

rs1554237658

Molecular consequence:

NM_001363725.2:c.3646C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001371656.1:c.6025C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001374820.1:c.6025C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001374828.1:c.6145C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_017519.3:c.5986C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_020732.3:c.5776C>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
SCV000745308	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus	criteria provided, single submitter (ACGS Guidelines, 2013)	Pathogenic (Mar 30, 2015)	germline	clinical testing	Citation Link,
SCV000745860	Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus	no assertion criteria provided (ACGS Guidelines, 2013)	Pathogenic (Oct 24, 2014)	germline	clinical testing	Citation Link,
SCV000807357	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 1, 2017)	de novo	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 25326635
SCV001433045	Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002054294	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]
SCV002578175	Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin See additional submitters CUBI - Core Unit Bioinformatics, Berlin Institute of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 27, 2022)	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	de novo	yes	not provided	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
not provided	germline	yes	1	not provided	not provided	1	not provided	clinical testing
not provided	unknown	yes	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

Molecular findings among patients referred for clinical whole-exome sequencing.

Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, Ward P, Braxton A, Wang M, Buhay C, Veeraraghavan N, Hawes A, Chiang T, Leduc M, Beuten J, Zhang J, He W, Scull J, Willis A, Landsverk M, Craigen WJ, Bekheirnia MR, et al.

JAMA. 2014 Nov 12;312(18):1870-9. doi: 10.1001/jama.2014.14601.

PubMed [citation]

PMID:: 25326635
PMCID:: PMC4326249

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 Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV000745308.1

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

#	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

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV000745860.1

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

#	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

From Baylor Genetics, SCV000807357.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing (GTR000508680.4)	PubMed (2)

Description

This nonsense mutation is categorized as deleterious according to ACMG guidelines (PMID:18414213). It was found once in our laboratory as a de novo finding in a 9-year-old female with intellectual disability, dysmorphic features, hyperextensibility, hirsutism, callosal dysgenesis.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	not provided	not provided	not provided	(GTR000508680.4)	not provided	not provided	not provided	not provided

From Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, SCV001433045.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	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	unknown	yes	1	not provided	not provided		1	not provided	not provided	not provided

From Genome-Nilou Lab, SCV002054294.1

#	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

From Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, SCV002578175.1

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

Last Updated: Apr 20, 2024

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