NM_000195.5(HPS1):c.769-14_834del AND Hermansky-Pudlak syndrome 1

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 10, 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:: RCV004573369.1

Allele description [Variation Report for NM_000195.5(HPS1):c.769-14_834del]

NM_000195.5(HPS1):c.769-14_834del

Gene:

HPS1:HPS1 biogenesis of lysosomal organelles complex 3 subunit 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10q24.2

Genomic location:

Preferred name:

NM_000195.5(HPS1):c.769-14_834del

HGVS:

NC_000010.11:g.98429828_98429907del
NG_009646.1:g.22045_22124del
NM_000195.5:c.769-14_834delMANE SELECT
NM_001311345.2:c.-105-261_-105-182del
NM_001322476.2:c.769-14_834del
NM_001322477.2:c.769-14_834del
NM_001322478.2:c.769-261_769-182del
NM_001322479.2:c.769-261_769-182del
NM_001322480.2:c.508-14_573del
NM_001322481.2:c.508-14_573del
NM_001322482.2:c.508-261_508-182del
NM_001322483.2:c.400-14_465del
NM_001322484.2:c.400-14_465del
NM_001322485.2:c.400-261_400-182del
NM_001322487.2:c.-204-14_-139del
NM_001322489.2:c.-105-261_-105-182del
NM_001322490.2:c.651-14_716del
NM_001322491.2:c.769-261_769-182del
NM_001322492.2:c.651-261_651-182del
NM_182639.4:c.769-14_834del
LRG_562t1:c.769-14_834del
LRG_562:g.22045_22124del
NC_000010.10:g.100189581_100189660del
NC_000010.10:g.100189585_100189664del

Molecular consequence:

NM_001311345.2:c.-105-261_-105-182del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322478.2:c.769-261_769-182del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322479.2:c.769-261_769-182del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322482.2:c.508-261_508-182del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322485.2:c.400-261_400-182del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322489.2:c.-105-261_-105-182del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322491.2:c.769-261_769-182del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322492.2:c.651-261_651-182del - intron variant - [Sequence Ontology: SO:0001627]
NM_000195.5:c.769-14_834del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322476.2:c.769-14_834del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322477.2:c.769-14_834del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322480.2:c.508-14_573del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322481.2:c.508-14_573del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322483.2:c.400-14_465del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322484.2:c.400-14_465del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322487.2:c.-204-14_-139del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322490.2:c.651-14_716del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_182639.4:c.769-14_834del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Hermansky-Pudlak syndrome 1 (HPS1)
Synonyms:: DELTA STORAGE POOL DISEASE
Identifiers:: MONDO: MONDO:0008748; MedGen: C2931875; Orphanet: 231500; Orphanet: 79430; OMIM: 203300

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005059705	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 10, 2023)	unknown	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

SCV005059705

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Nov 10, 2023)

unknown

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

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 Baylor Genetics, SCV005059705.1

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

#	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: Sep 29, 2024

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