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

Recent activity

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Rattus norvegicus Mycbp associated protein (Mycbpap), transcript variant 3, mRNA
Rattus norvegicus Mycbp associated protein (Mycbpap), transcript variant 3, mRNA
gi|2418774935|ref|NM_001415761.1|

Nucleotide
HMGB3 protein [Homo sapiens]
HMGB3 protein [Homo sapiens]
gi|47124341|gb|AAH70482.1|

Protein
AV246497 RIKEN full-length enriched, 0 day neonate head Mus musculus cDNA clone ...
AV246497 RIKEN full-length enriched, 0 day neonate head Mus musculus cDNA clone 4832410J21 3', mRNA sequence
gi|16387108|gnl|dbEST|9988441|dbj|A 97.2|

Nucleotide
LOC127898461 [Homo sapiens]
LOC127898461 [Homo sapiens]
Gene ID:127898461

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001582676	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 7, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 23830146, 24292712, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001582676

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 7, 2020)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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