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NM_006929.5(SKIC2):c.3464A>G (p.Asn1155Ser) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 16, 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:
RCV001371446.7

Allele description [Variation Report for NM_006929.5(SKIC2):c.3464A>G (p.Asn1155Ser)]

NM_006929.5(SKIC2):c.3464A>G (p.Asn1155Ser)

Gene:
SKIC2:SKI2 subunit of superkiller complex [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p21.33
Genomic location:
Preferred name:
NM_006929.5(SKIC2):c.3464A>G (p.Asn1155Ser)
HGVS:
  • NC_000006.12:g.31969344A>G
  • NG_032652.1:g.15541A>G
  • NM_006929.5:c.3464A>GMANE SELECT
  • NP_008860.4:p.Asn1155Ser
  • NC_000006.11:g.31937121A>G
Protein change:
N1155S
Links:
dbSNP: rs1445290831
NCBI 1000 Genomes Browser:
rs1445290831
Molecular consequence:
  • NM_006929.5:c.3464A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV001568011Labcorp Genetics (formerly Invitae), Labcorp
    criteria provided, single submitter

    (Invitae Variant Classification Sherloc (09022015))    		Uncertain significance
    (Oct 16, 2020)     		germlineclinical testing

    PubMed (1)
    [See all records that cite this PMID]

    Help

    Summary from all submissions

    EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
    not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

    Citations

    PubMed

    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, SCV001568011.4

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1not providednot providednot providednot providedclinical testing PubMed (1)

    Description

    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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with SKIV2L-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces asparagine with serine at codon 1155 of the SKIV2L protein (p.Asn1155Ser). The asparagine residue is weakly conserved and there is a small physicochemical difference between asparagine and serine.

    #SampleMethodObservation
    OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
    1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

    Last Updated: Sep 29, 2024