NM_024747.6(HPS6):c.19_20del (p.Leu7fs) AND Hermansky-Pudlak syndrome 6

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 30, 2017
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:: RCV000761514.2

Allele description [Variation Report for NM_024747.6(HPS6):c.19_20del (p.Leu7fs)]

NM_024747.6(HPS6):c.19_20del (p.Leu7fs)

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:

Microsatellite

Cytogenetic location:

10q24.32

Genomic location:

Preferred name:

NM_024747.6(HPS6):c.19_20del (p.Leu7fs)

HGVS:

NC_000010.11:g.102065491CT[1]
NG_012029.1:g.5102CT[1]
NM_024747.6:c.19_20delMANE SELECT
NP_079023.2:p.Leu7fs
LRG_564:g.5102CT[1]
NC_000010.10:g.103825248CT[1]
NM_024747.5:c.19_20delCT

Protein change:

L7fs

Links:

dbSNP: rs1590262288

NCBI 1000 Genomes Browser:

rs1590262288

Molecular consequence:

NM_024747.6:c.19_20del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Hermansky-Pudlak syndrome 6 (HPS6)
Identifiers:: MONDO: MONDO:0013558; MedGen: C3888007; Orphanet: 231512; Orphanet: 79430; OMIM: 614075

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000891643	Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Dec 30, 2017)	unknown	curation	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000891643

Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Dec 30, 2017)

unknown

curation

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	unknown	yes	not provided	not provided	not provided	not provided	not provided	curation

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University, SCV000891643.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (1)

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

Last Updated: Oct 14, 2023

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