VCV000985894.2 - ClinVar

NM_004746.4(DLGAP1):c.2925_2929del (p.Arg976fs)

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.

(1)

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.

Uncertain significance

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_004746.4(DLGAP1):c.2925_2929del (p.Arg976fs)

Variation ID: 985894 Accession: VCV000985894.2

Type and length

Deletion, 5 bp

Location

Cytogenetic: 18p11.31 18: 3499190-3499194 (GRCh38) [ NCBI UCSC ] 18: 3499188-3499192 (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	Nov 21, 2020	Jan 7, 2023	Jun 12, 2019

HGVS

Nucleotide	Protein	Molecular consequence
NM_004746.4:c.2925_2929del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_004737.2:p.Arg976fs	frameshift
NM_001003809.3:c.2019_2023del	NP_001003809.1:p.Arg674fs	frameshift
NM_001242762.2:c.1977_1981del	NP_001229691.1:p.Arg660fs	frameshift
NM_001242763.2:c.2091_2095del	NP_001229692.1:p.Arg698fs	frameshift
NM_001242764.2:c.2043_2047del	NP_001229693.1:p.Arg682fs	frameshift
NM_001242766.2:c.2049_2053del	NP_001229695.1:p.Arg684fs	frameshift
NM_001308390.2:c.2073_2077del	NP_001295319.1:p.Arg692fs	frameshift
NC_000018.10:g.3499191_3499195del
NC_000018.9:g.3499189_3499193del

... more HGVS ... less HGVS

Protein change

R660fs, R674fs, R682fs, R684fs, R692fs, R698fs, R976fs

Other names

Canonical SPDI

NC_000018.10:3499189:GCCGGG:G

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

dbSNP: rs2049797649 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.
DLGAP1		-	-	GRCh38 GRCh37	57	227

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.
Inborn genetic diseases	Uncertain significance (1)	criteria provided, single submitter	Jun 12, 2019	RCV001267043.2

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.
Uncertain significance (Jun 12, 2019)	criteria provided, single submitter (Ambry exome assertion method (8-5-2015)) Method: clinical testing	Inborn genetic diseases Affected status: yes Allele origin: germline	Ambry Genetics Accession: SCV001445224.2 First in ClinVar: Nov 21, 2020 Last updated: Jan 07, 2023	Publications: PubMed (1) PubMed: 12954649 Number of individuals with the variant: 1 Clinical Features: Autistic disorder of childhood onset (present) , Fatigue (present) , Nausea (present) , Drooling (present) , Depressivity (present) , Constipation (present) , Anxiety (present) , … (more) Autistic disorder of childhood onset (present) , Fatigue (present) , Nausea (present) , Drooling (present) , Depressivity (present) , Constipation (present) , Anxiety (present) , Incoordination (present) , Delayed speech and language development (present) , Mental deterioration (present) , Developmental regression (present) , Gait disturbance (present) , Decreased serum ceruloplasmin (present) , Elevated alkaline phosphatase (present) , Decreased body weight (present) (less) Sex: male Ethnicity/Population group: Caucasian

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.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Crystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization.	Im YJ	The Journal of biological chemistry	2003	PMID: 12954649

Text-mined citations for rs2049797649 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jan 07, 2023

ClinVar Genomic variation as it relates to human health

NM_004746.4(DLGAP1):c.2925_2929del (p.Arg976fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs2049797649 ...