VCV000029942.2 - ClinVar

NM_021120.4(DLG3):c.1092dup (p.Thr365fs)

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.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_021120.4(DLG3):c.1092dup (p.Thr365fs)

Variation ID: 29942 Accession: VCV000029942.2

Type and length

Duplication, 1 bp

Location

Cytogenetic: Xq13.1 X: 70451967-70451968 (GRCh38) [ NCBI UCSC ] X: 69671817-69671818 (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	Aug 24, 2021	Aug 24, 2021	Aug 1, 2004

HGVS

Nucleotide	Protein	Molecular consequence
NM_021120.4:c.1092dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_066943.2:p.Thr365fs	frameshift
NC_000023.11:g.70451973dup
NC_000023.10:g.69671823dup
NG_015849.2:g.12119dup

Protein change

T365fs

Other names

Canonical SPDI

NC_000023.11:70451967:CCCCCC:CCCCCCC

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

ClinGen: CA128783 OMIM: 300189.0003 dbSNP: rs398122846 VarSome

Comment on variant

NCBI staff reviewed the sequence information reported in PubMed 15185169 to determine the location of this allele on the current reference sequence. The sequencing in Fig. 1 annotated as 1325insC can be mapped to NM_021120.3:c.1092dupC.

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.
DLG3		Some evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	183	335

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 disability, X-linked 90	Pathogenic (1)	no assertion criteria provided	Aug 1, 2004	RCV000022834.23

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 (Aug 01, 2004)	no assertion criteria provided Method: literature only	INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED 90 Affected status: not provided Allele origin: germline	OMIM Accession: SCV000044123.2 First in ClinVar: Apr 04, 2013 Last updated: Aug 24, 2021	Publications: PubMed (1) PubMed: 15185169 Comment on evidence: In affected members of a family segregating nonsyndromic X-linked intellectual developmental disorder mapping to Xq13 (XLID90; 300850), Tarpey et al. (2004) found a 1-bp insertion … (more) In affected members of a family segregating nonsyndromic X-linked intellectual developmental disorder mapping to Xq13 (XLID90; 300850), Tarpey et al. (2004) found a 1-bp insertion (1325insC) in exon 7 of the DLG3 gene, resulting in a frameshift and a stop codon at position 377, removing 54% of the normally translated protein. The mutation was not found in 350 normal chromosomes. (less)

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
Mutations in the DLG3 gene cause nonsyndromic X-linked mental retardation.	Tarpey P	American journal of human genetics	2004	PMID: 15185169

Text-mined citations for rs398122846 ...

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 Aug 06, 2023

ClinVar Genomic variation as it relates to human health

NM_021120.4(DLG3):c.1092dup (p.Thr365fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs398122846 ...