NC_000001.10:g.(?_235850229)_(235872628_?)del AND Chédiak-Higashi syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 24, 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:: RCV004583902.1

Allele description [Variation Report for NC_000001.10:g.(?_235850229)_(235872628_?)del]

NC_000001.10:g.(?_235850229)_(235872628_?)del

Gene:: LYST:lysosomal trafficking regulator [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 1q42.3
Genomic location:: Chr1: 235850229 - 235872628 (on Assembly GRCh37)
Preferred name:: NC_000001.10:g.(?_235850229)_(235872628_?)del
HGVS:: NC_000001.10:g.(?_235850229)_(235872628_?)del
This HGVS expression did not pass validation

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005065020	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 24, 2023)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9215679, 11857544, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005065020

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 24, 2023)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Invitae, SCV005065020.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 44-48 of the LYST gene. This deletion is out-of-frame, and is expected to create a premature termination codon and result in an absent or disrupted protein product. Loss-of-function variants in LYST are known to be pathogenic (PMID: 9215679, 11857544). This variant has not been reported in the literature in individuals affected with LYST-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jul 7, 2024

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