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NM_000195.5(HPS1):c.398+5G>A AND Hermansky-Pudlak syndrome 1

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Oct 5, 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:
RCV000005601.8

Allele description [Variation Report for NM_000195.5(HPS1):c.398+5G>A]

NM_000195.5(HPS1):c.398+5G>A

Gene:
HPS1:HPS1 biogenesis of lysosomal organelles complex 3 subunit 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q24.2
Genomic location:
Preferred name:
NM_000195.5(HPS1):c.398+5G>A
HGVS:
  • NC_000010.11:g.98435267C>T
  • NG_009646.1:g.16681G>A
  • NM_000195.4:c.398+5G>A
  • NM_000195.5:c.398+5G>AMANE SELECT
  • NM_001311345.2:c.-519+5G>A
  • NM_001322476.2:c.398+5G>A
  • NM_001322477.2:c.398+5G>A
  • NM_001322478.2:c.398+5G>A
  • NM_001322479.2:c.398+5G>A
  • NM_001322480.2:c.255+368G>A
  • NM_001322481.2:c.255+368G>A
  • NM_001322482.2:c.255+368G>A
  • NM_001322483.2:c.29+368G>A
  • NM_001322484.2:c.29+368G>A
  • NM_001322485.2:c.29+368G>A
  • NM_001322487.2:c.-618+5G>A
  • NM_001322489.2:c.-519+368G>A
  • NM_001322490.2:c.398+5G>A
  • NM_001322491.2:c.398+5G>A
  • NM_001322492.2:c.398+5G>A
  • NM_182639.4:c.398+5G>A
  • LRG_562t1:c.398+5G>A
  • LRG_562:g.16681G>A
  • NC_000010.10:g.100195024C>T
  • NM_000195.2:c.398+5G>A
  • NM_000195.5:c.398+5G>A
Nucleotide change:
IVS5DS, G-A, +5
Links:
OMIM: 604982.0007; dbSNP: rs281865077
NCBI 1000 Genomes Browser:
rs281865077
Molecular consequence:
  • NM_000195.5:c.398+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001311345.2:c.-519+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322476.2:c.398+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322477.2:c.398+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322478.2:c.398+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322479.2:c.398+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322480.2:c.255+368G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322481.2:c.255+368G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322482.2:c.255+368G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322483.2:c.29+368G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322484.2:c.29+368G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322485.2:c.29+368G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322487.2:c.-618+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322489.2:c.-519+368G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322490.2:c.398+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322491.2:c.398+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322492.2:c.398+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_182639.4:c.398+5G>A - intron variant - [Sequence Ontology: SO:0001627]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000025783OMIM
no assertion criteria provided
Pathogenic
(Sep 1, 2000) 		germlineliterature only

PubMed (1)
[See all records that cite this PMID]

SCV000040531GeneReviews
no classification provided
not providedgermlineliterature only

SCV004199924Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Oct 5, 2023) 		unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Heterozygous HPS1 mutations in a case of Hermansky-Pudlak syndrome with giant melanosomes.

Horikawa T, Araki K, Fukai K, Ueda M, Ueda T, Ito S, Ichihashi M.

Br J Dermatol. 2000 Sep;143(3):635-40.

PubMed [citation]
PMID:
10971344

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 OMIM, SCV000025783.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

For discussion of the splice site mutation in the HPS1 gene (IVS5+5G-A) that was found in compound heterozygous state in a patient with Hermansky-Pudlak syndrome (HPS1; 203300) by Horikawa et al. (2000), see 604982.0006.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From GeneReviews, SCV000040531.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature onlynot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV004199924.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 12, 2024