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NM_001321075.3(DLG4):c.1961C>T (p.Ser654Phe) AND DLG4-related synaptopathy

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 19, 2021
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:
RCV001563644.4

Allele description [Variation Report for NM_001321075.3(DLG4):c.1961C>T (p.Ser654Phe)]

NM_001321075.3(DLG4):c.1961C>T (p.Ser654Phe)

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.1961C>T (p.Ser654Phe)
HGVS:
  • NC_000017.11:g.7191908G>A
  • NG_008391.2:g.33143C>T
  • NG_008391.3:g.33142C>T
  • NM_001128827.4:c.1952C>T
  • NM_001321074.1:c.2081C>T
  • NM_001321075.3:c.1961C>TMANE SELECT
  • NM_001321076.3:c.1781C>T
  • NM_001321077.3:c.1781C>T
  • NM_001365.5:c.2090C>T
  • NM_001369566.3:c.1880C>T
  • NP_001122299.1:p.Ser651Phe
  • NP_001308003.1:p.Ser694Phe
  • NP_001308004.1:p.Ser654Phe
  • NP_001308005.1:p.Ser594Phe
  • NP_001308006.1:p.Ser594Phe
  • NP_001356.1:p.Ser697Phe
  • NP_001356.1:p.Ser697Phe
  • NP_001356495.1:p.Ser627Phe
  • NC_000017.10:g.7095227G>A
  • NM_001365.4:c.2090C>T
Protein change:
S594F
Links:
dbSNP: rs752934560
NCBI 1000 Genomes Browser:
rs752934560
Molecular consequence:
  • NM_001128827.4:c.1952C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321074.1:c.2081C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321075.3:c.1961C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321076.3:c.1781C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321077.3:c.1781C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365.5:c.2090C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369566.3:c.1880C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
DLG4-related synaptopathy
Identifiers:

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001786631Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSLVariantClassificationCriteria RUGD 01 April 2020)		Uncertain significance
(Feb 19, 2021) 		unknownclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001786631.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The DLG4 c.2090C>T (p.Ser697Phe) variant is a missense variant. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. This variant is reported at a frequency of 0.000013 in the European (non-Finnish) population of the Genome Aggregation Database. However, this frequency is based on one allele in a region of good sequence coverage, so the variant is presumed to be rare. The p.Ser697Phe variant is located at a conserved residue in the guanylate kinase-like domain of the PSD-95 protein. In silico tools consistently predict a functional effect of this variant, but these predictions have not been tested experimentally. Based on the available evidence, the p.Ser697Phe variant is classified as a variant of uncertain significance for DLG4-related synaptopathy.

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

Last Updated: Dec 24, 2023