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NM_000081.4(LYST):c.10003C>T (p.Arg3335Cys) AND Chédiak-Higashi syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 8, 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:
RCV002010169.4

Allele description [Variation Report for NM_000081.4(LYST):c.10003C>T (p.Arg3335Cys)]

NM_000081.4(LYST):c.10003C>T (p.Arg3335Cys)

Genes:
LOC126806063:MED14-independent group 3 enhancer GRCh37_chr1:235871544-235872743 [Gene]
LYST:lysosomal trafficking regulator [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q42.3
Genomic location:
Preferred name:
NM_000081.4(LYST):c.10003C>T (p.Arg3335Cys)
HGVS:
  • NC_000001.11:g.235709231G>A
  • NG_007397.1:g.179410C>T
  • NM_000081.4:c.10003C>TMANE SELECT
  • NM_001301365.1:c.10003C>T
  • NP_000072.2:p.Arg3335Cys
  • NP_001288294.1:p.Arg3335Cys
  • LRG_143t2:c.10003C>T
  • LRG_143:g.179410C>T
  • LRG_143p2:p.Arg3335Cys
  • NC_000001.10:g.235872531G>A
Protein change:
R3335C
Molecular consequence:
  • NM_000081.4:c.10003C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001301365.1:c.10003C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Chédiak-Higashi syndrome (CHS)
Synonyms:
Chediak-Higashi Syndrome
Identifiers:
MONDO: MONDO:0008963; MedGen: C0007965; Orphanet: 167; OMIM: 214500

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002278679Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Mar 8, 2023) 		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, SCV002278679.3

#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 sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt LYST protein function. ClinVar contains an entry for this variant (Variation ID: 1491815). This variant has not been reported in the literature in individuals affected with LYST-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 3335 of the LYST protein (p.Arg3335Cys).

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

Last Updated: Sep 29, 2024