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NM_000195.5(HPS1):c.700C>T (p.Leu234=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000289325.6
Variation ID:
289325
Description:
single nucleotide variant
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NM_000195.5(HPS1):c.700C>T (p.Leu234=)

Allele ID
273562
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q24.2
Genomic location
10: 98430639 (GRCh38) GRCh38 UCSC
10: 100190396 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.100190396G>A
NC_000010.11:g.98430639G>A
NM_000195.5:c.700C>T MANE Select NP_000186.2:p.Leu234= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:98430638:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00046
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00039
The Genome Aggregation Database (gnomAD), exomes 0.00037
The Genome Aggregation Database (gnomAD) 0.00029
1000 Genomes Project 0.00020
Exome Aggregation Consortium (ExAC) 0.00046
Links
ClinGen: CA5639309
dbSNP: rs150444975
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV001105236.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 8, 2020 RCV000330842.4
Uncertain significance 1 no assertion criteria provided Apr 11, 2020 RCV001275297.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HPS1 - - GRCh38
GRCh37
400 419

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Hermansky-Pudlak syndrome 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001262170.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001053844.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Apr 10, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000343672.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Apr 11, 2020)
no assertion criteria provided
Method: clinical testing
Hermansky-Pudlak syndrome
Allele origin: germline
Natera, Inc.
Accession: SCV001460305.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=HPS1 - - - -

Text-mined citations for rs150444975...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated May 16, 2021