NM_014639.4(SKIC3):c.4507C>T (p.Arg1503Cys) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Nov 1, 2022
Review status:: criteria provided, conflicting classifications

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:: RCV000262565.28

Allele description [Variation Report for NM_014639.4(SKIC3):c.4507C>T (p.Arg1503Cys)]

NM_014639.4(SKIC3):c.4507C>T (p.Arg1503Cys)

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.4507C>T (p.Arg1503Cys)

Other names:

SKIC3, ARG1503CYS (rs200067423)

HGVS:

NC_000005.10:g.95467979G>A
NG_023414.1:g.92027C>T
NM_014639.4:c.4507C>TMANE SELECT
NP_055454.1:p.Arg1503Cys
NP_055454.1:p.Arg1503Cys
LRG_173t1:c.4507C>T
LRG_173:g.92027C>T
LRG_173p1:p.Arg1503Cys
NC_000005.9:g.94803683G>A
NM_014639.3:c.4507C>T

Protein change:

R1503C; ARG1503CYS

Links:

OMIM: 614589.0010; dbSNP: rs200067423

NCBI 1000 Genomes Browser:

rs200067423

Molecular consequence:

NM_014639.4:c.4507C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000341484	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Apr 14, 2016)	germline	clinical testing	Citation Link,
SCV001249413	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Mar 1, 2018)	germline	clinical testing	Citation Link,
SCV002310115	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 1, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 28292286, 34093558, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000341484

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Uncertain significance
(Apr 14, 2016)

germline

clinical testing

Citation Link,

SCV001249413

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Mar 1, 2018)

germline

clinical testing

Citation Link,

SCV002310115

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 1, 2022)

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	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa.

Kinnear C, Glanzmann B, Banda E, Schlechter N, Durrheim G, Neethling A, Nel E, Schoeman M, Johnson G, van Helden PD, Hoal EG, Esser M, Urban M, Möller M.

BMC Med Genet. 2017 Mar 14;18(1):26. doi: 10.1186/s12881-017-0388-5.

PubMed [citation]

PMID:: 28292286
PMCID:: PMC5351214

Clinical Utility of Whole Exome Sequencing and Targeted Panels for the Identification of Inborn Errors of Immunity in a Resource-Constrained Setting.

Engelbrecht C, Urban M, Schoeman M, Paarwater B, van Coller A, Abraham DR, Cornelissen H, Glashoff R, Esser M, Möller M, Kinnear C, Glanzmann B.

Front Immunol. 2021;12:665621. doi: 10.3389/fimmu.2021.665621.

PubMed [citation]

PMID:: 34093558
PMCID:: PMC8176954

See all PubMed Citations (3)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000341484.4

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

#	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		1	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV001249413.24

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

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

From Invitae, SCV002310115.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 1503 of the TTC37 protein (p.Arg1503Cys). This variant is present in population databases (rs200067423, gnomAD 0.04%). This missense change has been observed in individual(s) with trichohepatoenteric syndrome (PMID: 28292286, 34093558). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 287653). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Aug 4, 2024

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