NM_000081.4(LYST):c.2395_2396delinsAT (p.Gly799Ile) AND Chédiak-Higashi syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 15, 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:: RCV002297143.3

Allele description [Variation Report for NM_000081.4(LYST):c.2395_2396delinsAT (p.Gly799Ile)]

NM_000081.4(LYST):c.2395_2396delinsAT (p.Gly799Ile)

Gene:

LYST:lysosomal trafficking regulator [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

1q42.3

Genomic location:

Preferred name:

NM_000081.4(LYST):c.2395_2396delinsAT (p.Gly799Ile)

HGVS:

NC_000001.11:g.235806740_235806741delinsAT
NG_007397.1:g.81900_81901delinsAT
NM_000081.4:c.2395_2396delinsATMANE SELECT
NM_001301365.1:c.2395_2396delinsAT
NP_000072.2:p.Gly799Ile
NP_000072.2:p.Gly799Ile
NP_001288294.1:p.Gly799Ile
LRG_143t1:c.2395_2396delGGinsAT
LRG_143t2:c.2395_2396delinsAT
LRG_143:g.81900_81901delinsAT
LRG_143p1:p.Gly799Ile
LRG_143p2:p.Gly799Ile
NC_000001.10:g.235970040_235970041delinsAT
NM_000081.3:c.2395_2396delGGinsAT

Protein change:

G799I

Molecular consequence:

NM_000081.4:c.2395_2396delinsAT - missense variant - [Sequence Ontology: SO:0001583]
NM_001301365.1:c.2395_2396delinsAT - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002597645	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 15, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002597645

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 15, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Invitae, SCV002597645.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available"). This variant has not been reported in the literature in individuals affected with LYST-related conditions. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This sequence change replaces glycine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 799 of the LYST protein (p.Gly799Ile).

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

Last Updated: Feb 20, 2024

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