NM_014639.4(SKIC3):c.1374C>G (p.Tyr458Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 25, 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:: RCV001942202.6

Allele description [Variation Report for NM_014639.4(SKIC3):c.1374C>G (p.Tyr458Ter)]

NM_014639.4(SKIC3):c.1374C>G (p.Tyr458Ter)

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.1374C>G (p.Tyr458Ter)

HGVS:

NC_000005.10:g.95524543G>C
NG_023414.1:g.35463C>G
NM_014639.4:c.1374C>GMANE SELECT
NP_055454.1:p.Tyr458Ter
LRG_173:g.35463C>G
NC_000005.9:g.94860247G>C

Protein change:

Y458*

Links:

dbSNP: rs373796916

NCBI 1000 Genomes Browser:

rs373796916

Molecular consequence:

NM_014639.4:c.1374C>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002228197	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 25, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 20176027, 21120949, 29527791, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002228197

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 25, 2023)

germline

clinical testing

PubMed (4)
[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

Mutations in TTC37 cause trichohepatoenteric syndrome (phenotypic diarrhea of infancy).

Hartley JL, Zachos NC, Dawood B, Donowitz M, Forman J, Pollitt RJ, Morgan NV, Tee L, Gissen P, Kahr WH, Knisely AS, Watson S, Chitayat D, Booth IW, Protheroe S, Murphy S, de Vries E, Kelly DA, Maher ER.

Gastroenterology. 2010 Jun;138(7):2388-98, 2398.e1-2. doi: 10.1053/j.gastro.2010.02.010. Epub 2010 Feb 20.

PubMed [citation]

PMID:: 20176027
PMCID:: PMC3166659

Novel mutations in TTC37 associated with tricho-hepato-enteric syndrome.

Fabre A, Martinez-Vinson C, Roquelaure B, Missirian C, André N, Breton A, Lachaux A, Odul E, Colomb V, Lemale J, Cézard JP, Goulet O, Sarles J, Levy N, Badens C.

Hum Mutat. 2011 Mar;32(3):277-81. doi: 10.1002/humu.21420. Epub 2011 Feb 17.

PubMed [citation]

PMID:: 21120949

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002228197.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Tyr458*) in the TTC37 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TTC37 are known to be pathogenic (PMID: 20176027, 21120949). This variant is present in population databases (rs373796916, gnomAD 0.005%). This premature translational stop signal has been observed in individual(s) with trichohepatoenteric syndrome (PMID: 29527791). ClinVar contains an entry for this variant (Variation ID: 1455116). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as 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: Sep 29, 2024

ClinVar

Relating variation to medicine