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NM_001321075.3(DLG4):c.1977-2A>G AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 15, 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:
RCV001382597.13

Allele description [Variation Report for NM_001321075.3(DLG4):c.1977-2A>G]

NM_001321075.3(DLG4):c.1977-2A>G

Gene:
DLG4:discs large MAGUK scaffold protein 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17p13.1
Genomic location:
Preferred name:
NM_001321075.3(DLG4):c.1977-2A>G
HGVS:
  • NC_000017.11:g.7191360T>C
  • NG_008391.2:g.33691A>G
  • NG_008391.3:g.33690A>G
  • NM_001128827.4:c.1968-2A>G
  • NM_001321074.1:c.2097-2A>G
  • NM_001321075.3:c.1977-2A>GMANE SELECT
  • NM_001321076.3:c.1797-2A>G
  • NM_001321077.3:c.1797-2A>G
  • NM_001365.5:c.2106-2A>G
  • NM_001369566.3:c.1896-2A>G
  • NC_000017.10:g.7094679T>C
Links:
dbSNP: rs2142808860
NCBI 1000 Genomes Browser:
rs2142808860
Molecular consequence:
  • NM_001128827.4:c.1968-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001321074.1:c.2097-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001321075.3:c.1977-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001321076.3:c.1797-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001321077.3:c.1797-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001365.5:c.2106-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001369566.3:c.1896-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001581438Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 15, 2020) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability.

Lelieveld SH, Reijnders MR, Pfundt R, Yntema HG, Kamsteeg EJ, de Vries P, de Vries BB, Willemsen MH, Kleefstra T, Löhner K, Vreeburg M, Stevens SJ, van der Burgt I, Bongers EM, Stegmann AP, Rump P, Rinne T, Nelen MR, Veltman JA, Vissers LE, Brunner HG, Gilissen C.

Nat Neurosci. 2016 Sep;19(9):1194-6. doi: 10.1038/nn.4352. Epub 2016 Aug 1. Review.

PubMed [citation]
PMID:
27479843
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001581438.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change affects an acceptor splice site in intron 20 of the DLG4 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with clinical features of DLG4-related conditions (Invitae). In at least one individual the variant was observed to be de novo. Experimental studies and prediction algorithms are not available or were not evaluated, and the effect of this variant on mRNA splicing is currently unknown. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in DLG4 are known to be pathogenic (PMID: 27479843, 29460436). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 5, 2024