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NM_020458.4(TTC7A):c.192del (p.Phe64fs) AND Multiple gastrointestinal atresias

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 7, 2020
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001383525.5

Allele description [Variation Report for NM_020458.4(TTC7A):c.192del (p.Phe64fs)]

NM_020458.4(TTC7A):c.192del (p.Phe64fs)

Gene:
TTC7A:tetratricopeptide repeat domain 7A [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p21
Genomic location:
Preferred name:
NM_020458.4(TTC7A):c.192del (p.Phe64fs)
HGVS:
  • NC_000002.12:g.46950370del
  • NG_034143.2:g.39242del
  • NM_001288951.2:c.192del
  • NM_001288953.2:c.90del
  • NM_001288955.2:c.-713del
  • NM_020458.4:c.192delMANE SELECT
  • NP_001275880.1:p.Phe64fs
  • NP_001275882.1:p.Phe30fs
  • NP_065191.2:p.Phe64fs
  • LRG_1323t1:c.192del
  • LRG_1323:g.39242del
  • LRG_1323p1:p.Phe64fs
  • NC_000002.11:g.47177507del
  • NC_000002.11:g.47177509del
  • NM_001288951.1:c.192del
Protein change:
F30fs
Links:
dbSNP: rs1476031758
NCBI 1000 Genomes Browser:
rs1476031758
Molecular consequence:
  • NM_001288955.2:c.-713del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001288951.2:c.192del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001288953.2:c.90del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_020458.4:c.192del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Multiple gastrointestinal atresias
Synonyms:
Familial intestinal polyatresia syndrome; Multiple intestinal atresia
Identifiers:
MONDO: MONDO:0009465; MedGen: C0220744; Orphanet: 2300

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001582676Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Sep 7, 2020)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias.

Chen R, Giliani S, Lanzi G, Mias GI, Lonardi S, Dobbs K, Manis J, Im H, Gallagher JE, Phanstiel DH, Euskirchen G, Lacroute P, Bettinger K, Moratto D, Weinacht K, Montin D, Gallo E, Mangili G, Porta F, Notarangelo LD, Pedretti S, Al-Herz W, et al.

J Allergy Clin Immunol. 2013 Sep;132(3):656-664.e17. doi: 10.1016/j.jaci.2013.06.013. Epub 2013 Jul 4.

PubMed [citation]
PMID:
23830146
PMCID:
PMC3759618

TTC7A mutations disrupt intestinal epithelial apicobasal polarity.

Bigorgne AE, Farin HF, Lemoine R, Mahlaoui N, Lambert N, Gil M, Schulz A, Philippet P, Schlesser P, Abrahamsen TG, Oymar K, Davies EG, Ellingsen CL, Leteurtre E, Moreau-Massart B, Berrebi D, Bole-Feysot C, Nischke P, Brousse N, Fischer A, Clevers H, de Saint Basile G.

J Clin Invest. 2014 Jan;124(1):328-37.

PubMed [citation]
PMID:
24292712
PMCID:
PMC3871247
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001582676.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in TTC7A are known to be pathogenic (PMID: 23830146, 24292712). This variant has not been reported in the literature in individuals with TTC7A-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Phe64Leufs*15) in the TTC7A gene. It is expected to result in an absent or disrupted protein product.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024