VCV000190389.3 - ClinVar

NM_020458.4(TTC7A):c.764+1del

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_020458.4(TTC7A):c.764+1del

Variation ID: 190389 Accession: VCV000190389.3

Type and length

Deletion, 1 bp

Location

Cytogenetic: 2p21 2: 46978905 (GRCh38) [ NCBI UCSC ] 2: 47206047 (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	Feb 20, 2022	Feb 20, 2022	Sep 1, 2013

HGVS

Nucleotide	Protein	Molecular consequence
NM_020458.4:c.764+1del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice donor
NM_001288951.2:c.764+1del		splice donor
NM_001288953.2:c.662+1del		splice donor
NM_001288955.2:c.-141+1del		splice donor
NC_000002.12:g.46978908del
NC_000002.11:g.47206047del
NG_034143.2:g.67780del
LRG_1323:g.67780del
LRG_1323t1:c.764+1del

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000002.12:46978904:GGGG:GGG

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: CA10575703 OMIM: 609332.0009 dbSNP: rs886037746 VarSome

Comment on variant

NCBI staff reviewed the primers used to amplify the exons being sequenced (Table E1), and the report of the deleted product (PubMed 23830146). The G being deleted could have been exonic, or in the splice donor site. We chose to represent this as in the splice site.

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.
TTC7A		-	-	GRCh38 GRCh37	901	1051

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.
Gastrointestinal defects and immunodeficiency syndrome 1	Pathogenic (1)	no assertion criteria provided	Sep 1, 2013	RCV004562388.1

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 (Sep 01, 2013)	no assertion criteria provided Method: literature only	GASTROINTESTINAL DEFECTS AND IMMUNODEFICIENCY SYNDROME 1 Affected status: not provided Allele origin: germline	OMIM Accession: SCV000223092.4 First in ClinVar: May 23, 2015 Last updated: Feb 20, 2022	Publications: PubMed (1) PubMed: 23830146 Comment on evidence: For discussion of the 1-bp deletion (chr2.47,206,043delG, GRCh37) in exon 5 of the TTC7A gene (c.762delG) that was found in compound heterozygous state in a … (more) For discussion of the 1-bp deletion (chr2.47,206,043delG, GRCh37) in exon 5 of the TTC7A gene (c.762delG) that was found in compound heterozygous state in a patient with combined immunodeficiency and multiple intestinal atresia (GIDID1; 243150) by Chen et al. (2013), see 609332.0002. (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
Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias.	Chen R	The Journal of allergy and clinical immunology	2013	PMID: 23830146

Text-mined citations for rs886037746 ...

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 Oct 27, 2024

ClinVar Genomic variation as it relates to human health

NM_020458.4(TTC7A):c.764+1del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs886037746 ...