VCV000440892.1 - ClinVar

NM_001288951.1(TTC7A):c.[1616C>T];[2587G>A]

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

This genotype includes the following variants

NM_001288951.1(TTC7A):c.[1616C>T];[2587G>A]

Other names: -
Functional consequence: probably has functional consequence
Links: -

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	904	1054

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.
Multiple gastrointestinal atresias	Pathogenic (1)	no assertion criteria provided	Dec 5, 2016	RCV000664333.2

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.
Pathogenic (Dec 05, 2016)	no assertion criteria provided Method: clinical testing	Gastrointestinal defects and immunodeficiency syndrome 1 Gastrointestinal defects and immunodeficiency syndrome 1 (Autosomal recessive inheritance) Affected status: yes Allele origin: germline	Pediatrie Multidisciplinaire, Assitance Publique des Hopitaux de Marseille Study: Fondation Maladie Rare: High Throughput Sequencing and Rare Diseases septembre 2014 Accession: SCV000599796.1 First in ClinVar: Jul 29, 2018 Last updated: Jul 29, 2018	Publications: PubMed (1) PubMed: 29174094 Comment: Variant found in a Caucasian Girl born at 33 weeks gestation to unrelated parents with enteropathy requiring parenteral nutrition, facial dysmorphy, enamel dysplasia, hepatic abnormalities … (more) Variant found in a Caucasian Girl born at 33 weeks gestation to unrelated parents with enteropathy requiring parenteral nutrition, facial dysmorphy, enamel dysplasia, hepatic abnormalities and hypogammaglobulinemia. These feature are highly evocative of GASTROINTESTINAL DEFECTS AND IMMUNODEFICIENCY SYNDROME linked to TTC7A deficiency. (less) Sex: female Ethnicity/Population group: Caucasian Geographic origin: Portugal

Comment:

Variant found in a Caucasian Girl born at 33 weeks gestation to unrelated parents with enteropathy requiring parenteral nutrition, facial dysmorphy, enamel dysplasia, hepatic abnormalities and hypogammaglobulinemia. These feature are highly evocative of GASTROINTESTINAL DEFECTS AND IMMUNODEFICIENCY SYNDROME linked to TTC7A deficiency.

Germline Functional Evidence

Functional Help The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence	Method Help A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter.	Result Help A brief description of the result of this method for 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 functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
probably has functional consequence			Pediatrie Multidisciplinaire, Assitance Publique des Hopitaux de Marseille Study: Fondation Maladie Rare: High Throughput Sequencing and Rare Diseases septembre 2014 Accession: SCV000599796.1	Publications PubMed (1)

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Missense mutation of TTC7A mimicking tricho-hepato-enteric (SD/THE) syndrome in a patient with very-early onset inflammatory bowel disease.	Neves JF	European journal of medical genetics	2018	PMID: 29174094
Missense mutation of TTC7A mimicking tricho-hepato-enteric (SD/THE) syndrome in a patient with very-early onset inflammatory bowel disease.	Neves JF	European journal of medical genetics	2018	PMID: 29174094
Missense mutation of TTC7A mimicking tricho-hepato-enteric (SD/THE) syndrome in a patient with very-early onset inflammatory bowel disease.	Neves JF	European journal of medical genetics	2018	PMID: 29174094
TTC7A mutations disrupt intestinal epithelial apicobasal polarity.	Bigorgne AE	The Journal of clinical investigation	2014	PMID: 24292712

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_001288951.1(TTC7A):c.[1616C>T];[2587G>A]

Variant Details

NM_001288951.1(TTC7A):c.[1616C>T];[2587G>A]

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...