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NM_005101.4(ISG15):c.32C>T (p.Ala11Val) AND Mendelian susceptibility to mycobacterial diseases due to complete ISG15 deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 18, 2022
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:
RCV000819065.4

Allele description [Variation Report for NM_005101.4(ISG15):c.32C>T (p.Ala11Val)]

NM_005101.4(ISG15):c.32C>T (p.Ala11Val)

Gene:
ISG15:ISG15 ubiquitin like modifier [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.33
Genomic location:
Preferred name:
NM_005101.4(ISG15):c.32C>T (p.Ala11Val)
HGVS:
  • NC_000001.11:g.1014012C>T
  • NG_033033.2:g.17875C>T
  • NM_005101.4:c.32C>TMANE SELECT
  • NP_005092.1:p.Ala11Val
  • LRG_1231t1:c.32C>T
  • LRG_1231:g.17875C>T
  • LRG_1231p1:p.Ala11Val
  • NC_000001.10:g.949392C>T
  • NG_033033.1:g.5546C>T
  • NM_005101.3:c.32C>T
Protein change:
A11V
Links:
dbSNP: rs950572063
NCBI 1000 Genomes Browser:
rs950572063
Molecular consequence:
  • NM_005101.4:c.32C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Mendelian susceptibility to mycobacterial diseases due to complete ISG15 deficiency
Synonyms:
IMMUNODEFICIENCY 38, MYCOBACTERIOSIS, AUTOSOMAL RECESSIVE; ISG15 DEFICIENCY, AUTOSOMAL RECESSIVE; Immunodeficiency 38 with basal ganglia calcification; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0014502; MedGen: C4015293; Orphanet: 319563; OMIM: 616126

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000959707Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jun 18, 2022) 		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, SCV000959707.3

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

Description

This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 11 of the ISG15 protein (p.Ala11Val). This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with ISG15-related conditions. ClinVar contains an entry for this variant (Variation ID: 661610). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.

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

Last Updated: Sep 29, 2024