VCV001906639.4 - ClinVar

NM_000081.4(LYST):c.2539_2541del (p.Lys847del)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000081.4(LYST):c.2539_2541del (p.Lys847del)

Variation ID: 1906639 Accession: VCV001906639.4

Type and length

Deletion, 3 bp

Location

Cytogenetic: 1q42.3 1: 235806595-235806597 (GRCh38) [ NCBI UCSC ] 1: 235969895-235969897 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 7, 2023	Feb 4, 2024	Oct 13, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_000081.4:c.2539_2541del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000072.2:p.Lys847del	inframe deletion
NM_000081.3:c.2537_2539delAGA	NP_000072.2:p.Lys847del	inframe indel
NM_000081.3:c.2539_2541del
NM_001301365.1:c.2539_2541del	NP_001288294.1:p.Lys847del	inframe deletion
NC_000001.11:g.235806597_235806599del
NC_000001.10:g.235969897_235969899del
NG_007397.1:g.82044_82046del
LRG_143:g.82044_82046del
LRG_143t1:c.2539_2541del
LRG_143t2:c.2539_2541del	LRG_143p2:p.Lys847del

... more HGVS ... less HGVS

Protein change

K847del

Other names

Canonical SPDI

NC_000001.11:235806594:CTTCT:CT

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
LYST		-	-	GRCh38 GRCh37	3393	3531

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Chédiak-Higashi syndrome	Uncertain significance (2)	criteria provided, multiple submitters, no conflicts	Oct 13, 2022	RCV002587056.5

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Oct 13, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Chédiak-Higashi syndrome Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV002943279.1 First in ClinVar: Feb 07, 2023 Last updated: Feb 07, 2023	Comment: This variant, c.2539_2541del, results in the deletion of 1 amino acid(s) of the LYST protein (p.Lys847del), but otherwise preserves the integrity of the reading frame. … (more) This variant, c.2539_2541del, results in the deletion of 1 amino acid(s) of the LYST protein (p.Lys847del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs755119451, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with LYST-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. (less)
Uncertain significance (Nov 16, 2019)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Chédiak-Higashi syndrome Affected status: unknown Allele origin: germline	Revvity Omics, Revvity Accession: SCV003815239.2 First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024

Comment:

This variant, c.2539_2541del, results in the deletion of 1 amino acid(s) of the LYST protein (p.Lys847del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs755119451, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with LYST-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_000081.4(LYST):c.2539_2541del (p.Lys847del)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...