NM_021120.4(DLG3):c.1302+1G>A AND Intellectual disability, X-linked 90

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 1, 2004
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000012275.13

Allele description [Variation Report for NM_021120.4(DLG3):c.1302+1G>A]

NM_021120.4(DLG3):c.1302+1G>A

Genes:

DLG3-AS1:DLG3 antisense RNA 1 [Gene - HGNC]
DLG3:discs large MAGUK scaffold protein 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq13.1

Genomic location:

Preferred name:

NM_021120.4(DLG3):c.1302+1G>A

HGVS:

NC_000023.11:g.70453794G>A
NG_015849.2:g.13940G>A
NM_020730.3:c.291+1G>A
NM_021120.4:c.1302+1G>AMANE SELECT
NC_000023.10:g.69673644G>A

Nucleotide change:

IVS8DS, G-A, +1

Links:

OMIM: 300189.0002; dbSNP: rs1373474125

NCBI 1000 Genomes Browser:

rs1373474125

Molecular consequence:

NM_020730.3:c.291+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_021120.4:c.1302+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Intellectual disability, X-linked 90 (XLID90)
Synonyms:: INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED 90; DLG3-Related X-Linked Nonsyndromic Mental Retardation
Identifiers:: MONDO: MONDO:0010452; MedGen: C3275443; Orphanet: 777; OMIM: 300850

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000032509	OMIM	no assertion criteria provided	Pathogenic (Aug 1, 2004)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000032509

OMIM

no assertion criteria provided

Pathogenic
(Aug 1, 2004)

germline

literature only

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	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Mutations in the DLG3 gene cause nonsyndromic X-linked mental retardation.

Tarpey P, Parnau J, Blow M, Woffendin H, Bignell G, Cox C, Cox J, Davies H, Edkins S, Holden S, Korny A, Mallya U, Moon J, O'Meara S, Parker A, Stephens P, Stevens C, Teague J, Donnelly A, Mangelsdorf M, Mulley J, Partington M, et al.

Am J Hum Genet. 2004 Aug;75(2):318-24. Epub 2004 Jun 7.

PubMed [citation]

PMID:: 15185169
PMCID:: PMC1216066

Details of each submission

From OMIM, SCV000032509.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In affected members of a family with nonsyndromic X-linked intellectual developmental disorder mapping to Xq13 (XLID90; 300850), Tarpey et al. (2004) found a splice donor mutation in intron 8 of the DLG3 gene (1535+1G-A). The abnormal splicing was predicted to introduce a frameshift and a premature stop codon at position 383. The mutation was not found in 350 normal chromosomes.

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

Last Updated: Dec 24, 2023

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