NM_000195.5(HPS1):c.1065del (p.Asn356fs) AND Hermansky-Pudlak syndrome 1

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 26, 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:: RCV003468362.1

Allele description [Variation Report for NM_000195.5(HPS1):c.1065del (p.Asn356fs)]

NM_000195.5(HPS1):c.1065del (p.Asn356fs)

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.1065del (p.Asn356fs)

HGVS:

NC_000010.11:g.98425909del
NG_009646.1:g.26040del
NM_000195.5:c.1065delMANE SELECT
NM_001311345.2:c.93del
NM_001322476.2:c.1065del
NM_001322477.2:c.1065del
NM_001322478.2:c.966del
NM_001322479.2:c.966del
NM_001322480.2:c.804del
NM_001322481.2:c.804del
NM_001322482.2:c.705del
NM_001322483.2:c.696del
NM_001322484.2:c.696del
NM_001322485.2:c.597del
NM_001322487.2:c.93del
NM_001322489.2:c.93del
NP_000186.2:p.Asn356fs
NP_001298274.1:p.Asn32fs
NP_001309405.1:p.Asn356fs
NP_001309406.1:p.Asn356fs
NP_001309407.1:p.Asn323fs
NP_001309408.1:p.Asn323fs
NP_001309409.1:p.Asn269fs
NP_001309410.1:p.Asn269fs
NP_001309411.1:p.Asn236fs
NP_001309412.1:p.Asn233fs
NP_001309413.1:p.Asn233fs
NP_001309414.1:p.Asn200fs
NP_001309416.1:p.Asn32fs
NP_001309418.1:p.Asn32fs
LRG_562t1:c.1065del
LRG_562:g.26040del
LRG_562p1:p.Asn356fs
NC_000010.10:g.100185666del

Protein change:

N200fs

Molecular consequence:

NM_000195.5:c.1065del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001311345.2:c.93del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322476.2:c.1065del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322477.2:c.1065del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322478.2:c.966del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322479.2:c.966del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322480.2:c.804del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322481.2:c.804del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322482.2:c.705del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322483.2:c.696del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322484.2:c.696del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322485.2:c.597del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322487.2:c.93del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322489.2:c.93del - 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
SCV004199943	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 26, 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

SCV004199943

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jun 26, 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, SCV004199943.1

#	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: Dec 30, 2023

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