VCV002498092.3 - ClinVar

NM_001321075.3(DLG4):c.937C>T (p.Arg313Ter)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(3)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001321075.3(DLG4):c.937C>T (p.Arg313Ter)

Variation ID: 2498092 Accession: VCV002498092.3

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 17p13.1 17: 7196903 (GRCh38) [ NCBI UCSC ] 17: 7100222 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Apr 15, 2023	May 1, 2024	Mar 1, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001321075.3:c.937C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001308004.1:p.Arg313Ter	nonsense
NM_001128827.4:c.928C>T	NP_001122299.1:p.Arg310Ter	nonsense
NM_001321074.1:c.1057C>T	NP_001308003.1:p.Arg353Ter	nonsense
NM_001321076.3:c.757C>T	NP_001308005.1:p.Arg253Ter	nonsense
NM_001321077.3:c.757C>T	NP_001308006.1:p.Arg253Ter	nonsense
NM_001365.3:c.1066C>T
NM_001365.5:c.1066C>T	NP_001356.1:p.Arg356Ter	nonsense
NM_001369566.3:c.856C>T	NP_001356495.1:p.Arg286Ter	nonsense
NR_135527.1:n.2267C>T		non-coding transcript variant
NC_000017.11:g.7196903G>A
NC_000017.10:g.7100222G>A
NG_008391.3:g.28147C>T
NG_086977.1:g.911G>A

... more HGVS ... less HGVS

Protein change

R253*, R286*, R310*, R313*, R353*, R356*

Other names

Canonical SPDI

NC_000017.11:7196902:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
DLG4		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	158	328
LOC126862479	-	-	-	GRCh38	-	59

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Intellectual developmental disorder 62	Pathogenic (2)	criteria provided, multiple submitters, no conflicts	Sep 14, 2023	RCV003219153.2
Inborn genetic diseases	Pathogenic (1)	criteria provided, single submitter	Mar 1, 2024	RCV004285579.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Feb 28, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: research	Intellectual developmental disorder 62 Affected status: yes Allele origin: de novo	Tumer Group, Copenhagen University Hospital, Rigshospitalet Accession: SCV003915478.1 First in ClinVar: Apr 15, 2023 Last updated: Apr 15, 2023
Pathogenic (Sep 14, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Intellectual developmental disorder 62 Affected status: yes Allele origin: germline	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center Accession: SCV004099141.1 First in ClinVar: Oct 28, 2023 Last updated: Oct 28, 2023	Comment: PVS1, PS2, PM2
Pathogenic (Mar 01, 2024)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Inborn genetic diseases Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV004858072.1 First in ClinVar: May 01, 2024 Last updated: May 01, 2024	Comment: The c.1066C>T (p.R356) alteration, located in exon 11 (coding exon 11) of the DLG4 gene, consists of a C to T substitution at nucleotide position … (more) The c.1066C>T (p.R356) alteration, located in exon 11 (coding exon 11) of the DLG4 gene, consists of a C to T substitution at nucleotide position 1066. This changes the amino acid from a arginine (R) to a stop codon at amino acid position 356. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). Based on the available evidence, this alteration is classified as pathogenic. (less)

Comment:

The c.1066C>T (p.R356*) alteration, located in exon 11 (coding exon 11) of the DLG4 gene, consists of a C to T substitution at nucleotide position 1066. This changes the amino acid from a arginine (R) to a stop codon at amino acid position 356. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). Based on the available evidence, this alteration is classified as pathogenic.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated May 08, 2024

ClinVar Genomic variation as it relates to human health

NM_001321075.3(DLG4):c.937C>T (p.Arg313Ter)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...