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NM_004517.4(ILK):c.35A>G (p.Asn12Ser) AND Primary familial hypertrophic cardiomyopathy

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 18, 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:
RCV001364575.9

Allele description [Variation Report for NM_004517.4(ILK):c.35A>G (p.Asn12Ser)]

NM_004517.4(ILK):c.35A>G (p.Asn12Ser)

Genes:
LOC130005201:ATAC-STARR-seq lymphoblastoid active region 4345 [Gene]
ILK:integrin linked kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p15.4
Genomic location:
Preferred name:
NM_004517.4(ILK):c.35A>G (p.Asn12Ser)
HGVS:
  • NC_000011.10:g.6604306A>G
  • NG_029702.1:g.5573A>G
  • NM_001014794.3:c.35A>G
  • NM_001014795.3:c.35A>G
  • NM_001278441.2:c.35A>G
  • NM_001278442.2:c.-202A>G
  • NM_004517.4:c.35A>GMANE SELECT
  • NP_001014794.1:p.Asn12Ser
  • NP_001014795.1:p.Asn12Ser
  • NP_001265370.1:p.Asn12Ser
  • NP_004508.1:p.Asn12Ser
  • LRG_444:g.5573A>G
  • NC_000011.9:g.6625536A>G
Protein change:
N12S
Links:
dbSNP: rs765978022
NCBI 1000 Genomes Browser:
rs765978022
Molecular consequence:
  • NM_001278442.2:c.-202A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001014794.3:c.35A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001014795.3:c.35A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001278441.2:c.35A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004517.4:c.35A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Primary familial hypertrophic cardiomyopathy (HCM)
Synonyms:
Hereditary ventricular hypertrophy; Idiopathic hypertrophic subaortic stenosis
Identifiers:
MONDO: MONDO:0024573; MeSH: D024741; MedGen: C0949658; OMIM: PS192600

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001560731Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Feb 18, 2020)
germlineclinical testing

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

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, SCV001560731.5

#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 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"). This variant has not been reported in the literature in individuals with ILK-related conditions. This variant is present in population databases (rs765978022, ExAC 0.004%). This sequence change replaces asparagine with serine at codon 12 of the ILK protein (p.Asn12Ser). The asparagine residue is highly 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