NM_024747.6(HPS6):c.223C>T (p.Gln75Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 27, 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:: RCV001852027.4

Allele description [Variation Report for NM_024747.6(HPS6):c.223C>T (p.Gln75Ter)]

NM_024747.6(HPS6):c.223C>T (p.Gln75Ter)

Genes:

LOC130004578:ATAC-STARR-seq lymphoblastoid silent region 2738 [Gene]
HPS6:HPS6 biogenesis of lysosomal organelles complex 2 subunit 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q24.32

Genomic location:

Preferred name:

NM_024747.6(HPS6):c.223C>T (p.Gln75Ter)

HGVS:

NC_000010.11:g.102065697C>T
NG_012029.1:g.5308C>T
NM_024747.6:c.223C>TMANE SELECT
NP_079023.2:p.Gln75Ter
LRG_564:g.5308C>T
NC_000010.10:g.103825454C>T

Protein change:

Q75*; GLN75TER

Links:

OMIM: 607522.0007; dbSNP: rs281865107

NCBI 1000 Genomes Browser:

rs281865107

Molecular consequence:

NM_024747.6:c.223C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002233159	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 27, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19843503, 27225848, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002233159

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 27, 2023)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical and cellular characterisation of Hermansky-Pudlak syndrome type 6.

Huizing M, Pederson B, Hess RA, Griffin A, Helip-Wooley A, Westbroek W, Dorward H, O'Brien KJ, Golas G, Tsilou E, White JG, Gahl WA.

J Med Genet. 2009 Dec;46(12):803-10. doi: 10.1136/jmg.2008.065961. Epub 2009 Oct 20.

PubMed [citation]

PMID:: 19843503
PMCID:: PMC3500784

Novel HPS6 mutations identified by whole-exome sequencing in two Japanese sisters with suspected ocular albinism.

Miyamichi D, Asahina M, Nakajima J, Sato M, Hosono K, Nomura T, Negishi T, Miyake N, Hotta Y, Ogata T, Matsumoto N.

J Hum Genet. 2016 Sep;61(9):839-42. doi: 10.1038/jhg.2016.56. Epub 2016 May 26.

PubMed [citation]

PMID:: 27225848

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002233159.3

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

Description

This sequence change creates a premature translational stop signal (p.Gln75*) in the HPS6 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 701 amino acid(s) of the HPS6 protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with Hermansky-Pudlak syndrome (PMID: 19843503). ClinVar contains an entry for this variant (Variation ID: 30676). This variant disrupts a region of the HPS6 protein in which other variant(s) (p.Gln680*) have been determined to be pathogenic (PMID: 27225848). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. 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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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