NM_001374828.1(ARID1B):c.4795C>T (p.Gln1599Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 23, 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:: RCV002957709.2

Allele description [Variation Report for NM_001374828.1(ARID1B):c.4795C>T (p.Gln1599Ter)]

NM_001374828.1(ARID1B):c.4795C>T (p.Gln1599Ter)

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.4795C>T (p.Gln1599Ter)

HGVS:

NC_000006.12:g.157201020C>T
NG_066624.1:g.429995C>T
NM_001346813.1:c.4546C>T
NM_001363725.2:c.2296C>T
NM_001371656.1:c.4675C>T
NM_001374820.1:c.4675C>T
NM_001374828.1:c.4795C>TMANE SELECT
NM_017519.3:c.4636C>T
NM_020732.3:c.4426C>T
NM_175863.2:c.4213C>T
NP_001333742.1:p.Gln1516Ter
NP_001350654.1:p.Gln766Ter
NP_001358585.1:p.Gln1559Ter
NP_001361749.1:p.Gln1559Ter
NP_001361757.1:p.Gln1599Ter
NP_059989.3:p.Gln1546Ter
NP_065783.3:p.Gln1476Ter
NP_787059.2:p.Gln1405Ter
NC_000006.11:g.157522154C>T

Protein change:

Q1405*

Molecular consequence:

NM_001346813.1:c.4546C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001363725.2:c.2296C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001371656.1:c.4675C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001374820.1:c.4675C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001374828.1:c.4795C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_017519.3:c.4636C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_020732.3:c.4426C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_175863.2:c.4213C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV003272592	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 23, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 25674384, 30349098, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003272592

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 23, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

ARID1B-mediated disorders: Mutations and possible mechanisms.

Sim JC, White SM, Lockhart PJ.

Intractable Rare Dis Res. 2015 Feb;4(1):17-23. doi: 10.5582/irdr.2014.01021. Review.

PubMed [citation]

PMID:: 25674384
PMCID:: PMC4322591

The ARID1B spectrum in 143 patients: from nonsyndromic intellectual disability to Coffin-Siris syndrome.

van der Sluijs PJ, Jansen S, Vergano SA, Adachi-Fukuda M, Alanay Y, AlKindy A, Baban A, Bayat A, Beck-Wödl S, Berry K, Bijlsma EK, Bok LA, Brouwer AFJ, van der Burgt I, Campeau PM, Canham N, Chrzanowska K, Chu YWY, Chung BHY, Dahan K, De Rademaeker M, Destree A, et al.

Genet Med. 2019 Jun;21(6):1295-1307. doi: 10.1038/s41436-018-0330-z. Epub 2018 Nov 8. Erratum in: Genet Med. 2019 Sep;21(9):2160-2161. doi: 10.1038/s41436-018-0368-y.

PubMed [citation]

PMID:: 30349098
PMCID:: PMC6752273

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003272592.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with ARID1B-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln1476*) in the ARID1B gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ARID1B are known to be pathogenic (PMID: 25674384, 30349098).

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

Last Updated: Feb 20, 2024

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