U.S. flag

An official website of the United States government

NM_001321075.3(DLG4):c.1947del (p.Phe649fs) AND Intellectual developmental disorder 62

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Apr 4, 2024
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:
RCV004555946.1

Allele description [Variation Report for NM_001321075.3(DLG4):c.1947del (p.Phe649fs)]

NM_001321075.3(DLG4):c.1947del (p.Phe649fs)

Gene:
DLG4:discs large MAGUK scaffold protein 4 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
17p13.1
Genomic location:
Preferred name:
NM_001321075.3(DLG4):c.1947del (p.Phe649fs)
HGVS:
  • NC_000017.11:g.7191922del
  • NG_008391.2:g.33129del
  • NG_008391.3:g.33128del
  • NM_001128827.4:c.1938del
  • NM_001321074.1:c.2067del
  • NM_001321075.3:c.1947delMANE SELECT
  • NM_001321076.3:c.1767del
  • NM_001321077.3:c.1767del
  • NM_001365.5:c.2076del
  • NM_001369566.3:c.1866del
  • NP_001122299.1:p.Phe646fs
  • NP_001308003.1:p.Phe689fs
  • NP_001308004.1:p.Phe649fs
  • NP_001308005.1:p.Phe589fs
  • NP_001308006.1:p.Phe589fs
  • NP_001356.1:p.Phe692fs
  • NP_001356495.1:p.Phe622fs
  • NC_000017.10:g.7095241del
Protein change:
F589fs
Molecular consequence:
  • NM_001128827.4:c.1938del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001321074.1:c.2067del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001321075.3:c.1947del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001321076.3:c.1767del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001321077.3:c.1767del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001365.5:c.2076del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001369566.3:c.1866del - frameshift variant - [Sequence Ontology: SO:0001589]

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005045022Clinical Genomics Laboratory, Washington University in St. Louis
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Apr 4, 2024) 		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 Clinical Genomics Laboratory, Washington University in St. Louis, SCV005045022.1

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

Description

The DLG4 c.1947del (p.Phe649Leufs*11) variant, to our knowledge, has not been reported in the medical literature and is absent from the general population (gnomAD v.2.1.1), indicating it is not a common variant. This variant causes a frameshift by deleting a single nucleotide, leading to a premature termination codon, which is predicted to lead to nonsense mediated decay. Additionally, another variant that introduces a premature termination codon occurring C-terminal to this variant has been described in an affected individual and is considered pathogenic. Based on available information and the ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as likely pathogenic.

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

Last Updated: May 26, 2024