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NM_032383.5(HPS3):c.1163+1G>A

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Mar 28, 2019)
Last evaluated:
Nov 8, 2018
Accession:
VCV000004609.3
Variation ID:
4609
Description:
single nucleotide variant
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NM_032383.5(HPS3):c.1163+1G>A

Allele ID
19648
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3q24
Genomic location
3: 149145547 (GRCh38) GRCh38 UCSC
3: 148863334 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.148863334G>A
NC_000003.12:g.149145547G>A
NM_032383.5:c.1163+1G>A splice donor
... more HGVS
Protein change
-
Other names
1303, G-A, +1
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00005
The Genome Aggregation Database (gnomAD), exomes 0.00008
Exome Aggregation Consortium (ExAC) 0.00009
The Genome Aggregation Database (gnomAD) 0.00006
Links
ClinGen: CA340269
OMIM: 606118.0002
dbSNP: rs201227603
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, multiple submitters, no conflicts Oct 16, 2018 RCV000724652.2
Pathogenic 1 criteria provided, single submitter Nov 8, 2018 RCV000826142.1
Pathogenic 2 no assertion criteria provided Oct 11, 2012 RCV000004872.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HPS3 - - GRCh38
GRCh37
52 113

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Oct 16, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000936866.1
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change affects a donor splice site in intron 5 of the HPS3 gene. It is expected to disrupt RNA splicing and likely results ... (more)
Pathogenic
(Nov 08, 2018)
criteria provided, single submitter
Method: clinical testing
Hermansky-Pudlak syndrome
(Autosomal recessive inheritance)
Allele origin: germline
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine
Accession: SCV000967672.1
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (2)
Comment:
The c.1163+1G>A variant, also known as c.1303+1G>A, in HPS3 has been reported in the homozygous state in 3 individuals with Hermansky Pudlak syndrome type 3 ... (more)
Pathogenic
(Feb 16, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics
Accession: SCV000331832.4
Submitted: (Sep 19, 2018)
Evidence details
Publications
PubMed (1)
Other databases
http://www.egl-eurofins.com/em...
Pathogenic
(Nov 01, 2001)
no assertion criteria provided
Method: literature only
HERMANSKY-PUDLAK SYNDROME 3
Allele origin: germline
OMIM
Accession: SCV000025048.3
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)
pathologic
(Oct 11, 2012)
no assertion criteria provided
Method: curation
Hermansky-Pudlak Syndrome
Allele origin: not provided
GeneReviews
Accession: SCV000041519.1
Submitted: (Jan 08, 2013)
Evidence details
Comment:
Converted during submission to Pathogenic.

Citations for this variant

Title Author Journal Year Link
Hermansky-Pudlak Syndrome Huizing M - 2017 PMID: 20301464
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Xiong HY Science (New York, N.Y.) 2015 PMID: 25525159
Hermansky-Pudlak syndrome type 3 in Ashkenazi Jews and other non-Puerto Rican patients with hypopigmentation and platelet storage-pool deficiency. Huizing M American journal of human genetics 2001 PMID: 11590544
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=HPS3 - - - -

Record last updated Oct 27, 2019