NM_014639.4(SKIC3):c.2018G>A (p.Gly673Asp) AND Trichohepatoenteric syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 23, 2023
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:: RCV003317528.1

Allele description [Variation Report for NM_014639.4(SKIC3):c.2018G>A (p.Gly673Asp)]

NM_014639.4(SKIC3):c.2018G>A (p.Gly673Asp)

Gene:

SKIC3:SKI3 subunit of superkiller complex [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q15

Genomic location:

Preferred name:

NM_014639.4(SKIC3):c.2018G>A (p.Gly673Asp)

HGVS:

NC_000005.10:g.95520812C>T
NG_023414.1:g.39194G>A
NM_014639.4:c.2018G>AMANE SELECT
NP_055454.1:p.Gly673Asp
LRG_173t1:c.2018G>A
LRG_173:g.39194G>A
NC_000005.9:g.94856516C>T
NM_014639.3:c.2018G>A

Protein change:

G673D

Links:

dbSNP: rs769075304

NCBI 1000 Genomes Browser:

rs769075304

Molecular consequence:

NM_014639.4:c.2018G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Trichohepatoenteric syndrome
Synonyms:: THE SYNDROME; Syndromic diarrhea; Tricho-hepato-enteric syndrome
Identifiers:: MONDO: MONDO:0009105; MedGen: C1857276; Orphanet: 84064; OMIM: PS222470

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INSIG2 insulin induced gene 2 [Homo sapiens]
INSIG2 insulin induced gene 2 [Homo sapiens]
Gene ID:51141

Gene
(INSIG2[Gene Name]) AND Homo sapiens[Organism] AND (alive[prop]) (1)
Gene
BNIP3 BCL2 interacting protein 3 [Homo sapiens]
BNIP3 BCL2 interacting protein 3 [Homo sapiens]
Gene ID:664

Gene
(BNIP3[Gene Name]) AND Homo sapiens[Organism] AND (alive[prop]) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004021106	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely pathogenic (Jun 23, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 27302973, 35108801 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004021106

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely pathogenic
(Jun 23, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

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

Phenotypic and Genotypic Characterisation of Inflammatory Bowel Disease Presenting Before the Age of 2 years.

Kammermeier J, Dziubak R, Pescarin M, Drury S, Godwin H, Reeve K, Chadokufa S, Huggett B, Sider S, James C, Acton N, Cernat E, Gasparetto M, Noble-Jamieson G, Kiparissi F, Elawad M, Beales PL, Sebire NJ, Gilmour K, Uhlig HH, Bacchelli C, Shah N.

J Crohns Colitis. 2017 Jan;11(1):60-69. doi: 10.1093/ecco-jcc/jjw118. Epub 2016 Jun 14.

PubMed [citation]

PMID:: 27302973
PMCID:: PMC5885808

Tricho-Hepato-Eenteric Syndrome: Same Genotype but Different Phenotypes in Two Pakistani Children.

Waheed N, Saeed A, Cheema HA.

J Coll Physicians Surg Pak. 2022 Feb;32(2):242-246. doi: 10.29271/jcpsp.2022.02.242.

PubMed [citation]

PMID:: 35108801

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004021106.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Variant summary: TTC37 c.2018G>A (p.Gly673Asp) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 250248 control chromosomes. c.2018G>A has been reported in the literature in homozygous and compound heterozygous individuals affected with Trichohepatoenteric Syndrome (examples: Kammermeier_2017, Waheed_2022). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 27302973, 35108801). No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

#	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: Dec 24, 2023

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