NM_000195.5(HPS1):c.1925del (p.Gly642fs) AND Hermansky-Pudlak syndrome 1

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Oct 21, 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:: RCV003469647.1

Allele description [Variation Report for NM_000195.5(HPS1):c.1925del (p.Gly642fs)]

NM_000195.5(HPS1):c.1925del (p.Gly642fs)

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.1925del (p.Gly642fs)

Other names:

p.Gly642Glufs*83

HGVS:

NC_000010.11:g.98418192del
NG_009646.1:g.33758del
NM_000195.5:c.1925delMANE SELECT
NM_001311345.2:c.953del
NM_001322476.2:c.1925del
NM_001322477.2:c.1925del
NM_001322478.2:c.1826del
NM_001322479.2:c.1826del
NM_001322480.2:c.1664del
NM_001322481.2:c.1664del
NM_001322482.2:c.1565del
NM_001322483.2:c.1556del
NM_001322484.2:c.1556del
NM_001322485.2:c.1457del
NM_001322487.2:c.953del
NM_001322489.2:c.953del
NP_000186.2:p.Gly642fs
NP_001298274.1:p.Gly318fs
NP_001309405.1:p.Gly642fs
NP_001309406.1:p.Gly642fs
NP_001309407.1:p.Gly609fs
NP_001309408.1:p.Gly609fs
NP_001309409.1:p.Gly555fs
NP_001309410.1:p.Gly555fs
NP_001309411.1:p.Gly522fs
NP_001309412.1:p.Gly519fs
NP_001309413.1:p.Gly519fs
NP_001309414.1:p.Gly486fs
NP_001309416.1:p.Gly318fs
NP_001309418.1:p.Gly318fs
LRG_562t1:c.1925del
LRG_562:g.33758del
LRG_562p1:p.Gly642fs
NC_000010.10:g.100177947del
NC_000010.10:g.100177949del
NM_000195.3:c.1925del
NM_000195.3:c.1925delG
NM_000195.4:c.1925delG

Protein change:

G318fs

Links:

dbSNP: rs2136083690

NCBI 1000 Genomes Browser:

rs2136083690

Molecular consequence:

NM_000195.5:c.1925del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001311345.2:c.953del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322476.2:c.1925del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322477.2:c.1925del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322478.2:c.1826del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322479.2:c.1826del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322480.2:c.1664del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322481.2:c.1664del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322482.2:c.1565del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322483.2:c.1556del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322484.2:c.1556del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322485.2:c.1457del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322487.2:c.953del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322489.2:c.953del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV004199920	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 21, 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

SCV004199920

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 21, 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, SCV004199920.1

#	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: Nov 24, 2024

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