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NM_001321075.3(DLG4):c.478G>T (p.Glu160Ter) AND Intellectual developmental disorder 62

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Feb 28, 2023
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:
RCV001800192.3

Allele description [Variation Report for NM_001321075.3(DLG4):c.478G>T (p.Glu160Ter)]

NM_001321075.3(DLG4):c.478G>T (p.Glu160Ter)

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.478G>T (p.Glu160Ter)
HGVS:
  • NC_000017.11:g.7203451C>A
  • NG_008391.2:g.21600G>T
  • NG_008391.3:g.21599G>T
  • NM_001128827.4:c.469G>T
  • NM_001321074.1:c.598G>T
  • NM_001321075.3:c.478G>TMANE SELECT
  • NM_001321076.3:c.298G>T
  • NM_001321077.3:c.298G>T
  • NM_001365.5:c.607G>T
  • NM_001369566.3:c.397G>T
  • NP_001122299.1:p.Glu157Ter
  • NP_001308003.1:p.Glu200Ter
  • NP_001308004.1:p.Glu160Ter
  • NP_001308005.1:p.Glu100Ter
  • NP_001308006.1:p.Glu100Ter
  • NP_001356.1:p.Glu203Ter
  • NP_001356.1:p.Glu203Ter
  • NP_001356495.1:p.Glu133Ter
  • NC_000017.10:g.7106770C>A
  • NM_001321075.3:c.478G>T
  • NM_001365.4:c.607G>T
  • NR_135527.1:n.1808G>T
Protein change:
E100*
Links:
dbSNP: rs2142885279
NCBI 1000 Genomes Browser:
rs2142885279
Molecular consequence:
  • NR_135527.1:n.1808G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001128827.4:c.469G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001321074.1:c.598G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001321075.3:c.478G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001321076.3:c.298G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001321077.3:c.298G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001365.5:c.607G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001369566.3:c.397G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Intellectual developmental disorder 62
Synonyms:
MENTAL RETARDATION, AUTOSOMAL DOMINANT 62; INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 62
Identifiers:
MONDO: MONDO:0032919; MedGen: C5394083; OMIM: 618793

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002044331Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 21, 2021)
de novoresearch

PubMed (2)
[See all records that cite these PMIDs]

SCV002760122Laboratory of Medical Genetics, University of Torino - NeuroWES
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Nov 29, 2022)
germlineresearch

PubMed (1)
[See all records that cite this PMID]

SCV003915459Tumer Group, Copenhagen University Hospital, Rigshospitalet
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 28, 2023)
de novoresearch

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedresearch
not providedde novoyesnot providednot providednot providednot providednot providedresearch

Citations

PubMed

DLG4-related synaptopathy: a new rare brain disorder.

Rodríguez-Palmero A, Boerrigter MM, Gómez-Andrés D, Aldinger KA, Marcos-Alcalde Í, Popp B, Everman DB, Lovgren AK, Arpin S, Bahrambeigi V, Beunders G, Bisgaard AM, Bjerregaard VA, Bruel AL, Challman TD, Cogné B, Coubes C, de Man SA, Denommé-Pichon AS, Dye TJ, Elmslie F, Feuk L, et al.

Genet Med. 2021 May;23(5):888-899. doi: 10.1038/s41436-020-01075-9. Epub 2021 Feb 17.

PubMed [citation]
PMID:
33597769

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 Institute of Human Genetics, University of Leipzig Medical Center, SCV002044331.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot providednot providednot providednot providednot provided

From Laboratory of Medical Genetics, University of Torino - NeuroWES, SCV002760122.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Tumer Group, Copenhagen University Hospital, Rigshospitalet, SCV003915459.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 24, 2023