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NM_001321075.3(DLG4):c.1690C>T (p.Pro564Ser) AND Intellectual developmental disorder 62

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 2, 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:
RCV002470176.1

Allele description

NM_001321075.3(DLG4):c.1690C>T (p.Pro564Ser)

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.1690C>T (p.Pro564Ser)
HGVS:
  • NC_000017.11:g.7193486G>A
  • NG_008391.2:g.31565C>T
  • NG_008391.3:g.31564C>T
  • NM_001128827.4:c.1681C>T
  • NM_001321074.1:c.1810C>T
  • NM_001321075.3:c.1690C>TMANE SELECT
  • NM_001321076.3:c.1510C>T
  • NM_001321077.3:c.1510C>T
  • NM_001365.5:c.1819C>T
  • NM_001369566.3:c.1609C>T
  • NP_001122299.1:p.Pro561Ser
  • NP_001308003.1:p.Pro604Ser
  • NP_001308004.1:p.Pro564Ser
  • NP_001308005.1:p.Pro504Ser
  • NP_001308006.1:p.Pro504Ser
  • NP_001356.1:p.Pro607Ser
  • NP_001356.1:p.Pro607Ser
  • NP_001356495.1:p.Pro537Ser
  • NC_000017.10:g.7096805G>A
  • NM_001321075.1:c.1690C>T
  • NM_001365.4:c.1819C>T
  • NR_135527.1:n.3020C>T
Protein change:
P504S
Molecular consequence:
  • NM_001128827.4:c.1681C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321074.1:c.1810C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321075.3:c.1690C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321076.3:c.1510C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321077.3:c.1510C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365.5:c.1819C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369566.3:c.1609C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_135527.1:n.3020C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002769475Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Sep 2, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002769475.1

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

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3A. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with intellectual developmental disorder 62 (MIM#618793). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from proline to serine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0603 - Missense variant in a region that is highly intolerant to missense variation (high constraint region in DECIPHER). (SP) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0807 - This variant has no previous evidence of pathogenicity. (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

Last Updated: May 20, 2023