NM_001321075.3(DLG4):c.1292del (p.Phe431fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 12, 2018
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:: RCV001008937.1

Allele description [Variation Report for NM_001321075.3(DLG4):c.1292del (p.Phe431fs)]

NM_001321075.3(DLG4):c.1292del (p.Phe431fs)

Genes:

LOC126862479:MED14-independent group 3 enhancer GRCh37_chr17:7099412-7100611 [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.1292del (p.Phe431fs)

HGVS:

NC_000017.11:g.7196231del
NG_008391.2:g.28822del
NG_008391.3:g.28821del
NG_086977.1:g.239del
NM_001128827.4:c.1283del
NM_001321074.1:c.1412del
NM_001321075.3:c.1292delMANE SELECT
NM_001321076.3:c.1112del
NM_001321077.3:c.1112del
NM_001365.5:c.1419delT
NM_001369566.3:c.1211del
NP_001122299.1:p.Phe428fs
NP_001308003.1:p.Phe471fs
NP_001308004.1:p.Phe431fs
NP_001308005.1:p.Phe371fs
NP_001308006.1:p.Phe371fs
NP_001356.1:p.Phe474Serfs
NP_001356.1:p.Phe474fs
NP_001356495.1:p.Phe404fs
NC_000017.10:g.7099550del
NM_001365.3:c.1421delT
NM_001365.4:c.1421del
NR_135527.1:n.2622del

Protein change:

F371fs

Links:

dbSNP: rs1597451690

NCBI 1000 Genomes Browser:

rs1597451690

Molecular consequence:

NM_001128827.4:c.1283del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001321074.1:c.1412del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001321075.3:c.1292del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001321076.3:c.1112del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001321077.3:c.1112del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001365.5:c.1419delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001369566.3:c.1211del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_135527.1:n.2622del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001168744	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Jul 12, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001168744

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Jul 12, 2018)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV001168744.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.1421delT variant in the DLG4 gene has not been reported previously as a pathogenic variant nor as a benign variant to our knowledge. The c.1421delT variant causes a frameshift starting with codon Phenylalanine 474, changes this amino acid to a Serine residue, and creates a premature Stop codon at position 18 of the new reading frame, denoted p.Phe474SerfsX18. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1421delT variant is not observed in large population cohorts (Lek et al., 2016). Additionally, this variant has occurred de novo in this individual whose reported history is consistent with a DLG4-related disorder. The c.1421delT variant is considered a pathogenic variant.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 20, 2023

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