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NM_000081.4(LYST):c.10062_10063del (p.Ile3354fs) AND Chédiak-Higashi syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 26, 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:
RCV003066994.3

Allele description [Variation Report for NM_000081.4(LYST):c.10062_10063del (p.Ile3354fs)]

NM_000081.4(LYST):c.10062_10063del (p.Ile3354fs)

Genes:
LOC126806063:MED14-independent group 3 enhancer GRCh37_chr1:235871544-235872743 [Gene]
LYST:lysosomal trafficking regulator [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1q42.3
Genomic location:
Preferred name:
NM_000081.4(LYST):c.10062_10063del (p.Ile3354fs)
HGVS:
  • NC_000001.11:g.235709172_235709173del
  • NG_007397.1:g.179469_179470del
  • NG_082387.1:g.1029_1030del
  • NM_000081.2:c.10062_10063delCT
  • NM_000081.4:c.10062_10063delMANE SELECT
  • NM_001301365.1:c.10062_10063del
  • NP_000072.2:p.Ile3354Metfs
  • NP_000072.2:p.Ile3354fs
  • NP_001288294.1:p.Ile3354fs
  • LRG_143t1:c.10061_10062del
  • LRG_143t2:c.10062_10063del
  • LRG_143:g.179469_179470del
  • LRG_143p1:p.Ile3354Metfs
  • LRG_143p2:p.Ile3354fs
  • NC_000001.10:g.235872471_235872472del
  • NC_000001.10:g.235872472_235872473del
  • NM_000081.3:c.10061_10062delTC
Protein change:
I3354fs
Molecular consequence:
  • NM_000081.4:c.10062_10063del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001301365.1:c.10062_10063del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV003454492Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 26, 2022) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Mutations in the Chediak-Higashi syndrome gene (CHS1) indicate requirement for the complete 3801 amino acid CHS protein.

Karim MA, Nagle DL, Kandil HH, Bürger J, Moore KJ, Spritz RA.

Hum Mol Genet. 1997 Jul;6(7):1087-9.

PubMed [citation]
PMID:
9215679

Apparent genotype-phenotype correlation in childhood, adolescent, and adult Chediak-Higashi syndrome.

Karim MA, Suzuki K, Fukai K, Oh J, Nagle DL, Moore KJ, Barbosa E, Falik-Borenstein T, Filipovich A, Ishida Y, Kivrikko S, Klein C, Kreuz F, Levin A, Miyajima H, Regueiro JR, Russo C, Uyama E, Vierimaa O, Spritz RA.

Am J Med Genet. 2002 Feb 15;108(1):16-22.

PubMed [citation]
PMID:
11857544
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003454492.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. 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 creates a premature translational stop signal (p.Ile3354Metfs*5) in the LYST gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LYST are known to be pathogenic (PMID: 9215679, 11857544).

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

Last Updated: Sep 29, 2024