NM_006929.5(SKIC2):c.239_240del (p.Lys80fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 22, 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:: RCV003559034.2

Allele description [Variation Report for NM_006929.5(SKIC2):c.239_240del (p.Lys80fs)]

NM_006929.5(SKIC2):c.239_240del (p.Lys80fs)

Gene:

SKIC2:SKI2 subunit of superkiller complex [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

6p21.33

Genomic location:

Preferred name:

NM_006929.5(SKIC2):c.239_240del (p.Lys80fs)

HGVS:

NC_000006.12:g.31960222_31960223del
NG_032652.1:g.6419_6420del
NM_006929.5:c.239_240delMANE SELECT
NP_008860.4:p.Lys80fs
NC_000006.11:g.31927997_31927998del
NC_000006.11:g.31927999_31928000del

Protein change:

K80fs

Molecular consequence:

NM_006929.5:c.239_240del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV004278868	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 22, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22444670, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004278868

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 22, 2023)

germline

clinical testing

PubMed (2)
[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

SKIV2L mutations cause syndromic diarrhea, or trichohepatoenteric syndrome.

Fabre A, Charroux B, Martinez-Vinson C, Roquelaure B, Odul E, Sayar E, Smith H, Colomb V, Andre N, Hugot JP, Goulet O, Lacoste C, Sarles J, Royet J, Levy N, Badens C.

Am J Hum Genet. 2012 Apr 6;90(4):689-92. doi: 10.1016/j.ajhg.2012.02.009. Epub 2012 Mar 22.

PubMed [citation]

PMID:: 22444670
PMCID:: PMC3322239

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004278868.1

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

Description

This sequence change creates a premature translational stop signal (p.Lys80Metfs*81) in the SKIV2L gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SKIV2L are known to be pathogenic (PMID: 22444670). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SKIV2L-related conditions. 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

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