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NM_000271.5(NPC1):c.1300C>T (p.Pro434Ser)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Sep 29, 2021)
Last evaluated:
Nov 22, 2020
Accession:
VCV000092700.8
Variation ID:
92700
Description:
single nucleotide variant
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NM_000271.5(NPC1):c.1300C>T (p.Pro434Ser)

Allele ID
98607
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
18q11.2
Genomic location
18: 23556269 (GRCh38) GRCh38 UCSC
18: 21136233 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000018.10:g.23556269G>A
NC_000018.9:g.21136233G>A
NG_012795.1:g.35349C>T
... more HGVS
Protein change
P434S
Other names
-
Canonical SPDI
NC_000018.10:23556268:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.01138 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.01305
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01453
Exome Aggregation Consortium (ExAC) 0.00387
1000 Genomes Project 0.01138
The Genome Aggregation Database (gnomAD), exomes 0.00329
The Genome Aggregation Database (gnomAD) 0.01172
Trans-Omics for Precision Medicine (TOPMed) 0.01323
Trans-Omics for Precision Medicine (TOPMed) 0.01346
Links
ClinGen: CA145949
UniProtKB: O15118#VAR_043198
dbSNP: rs61731962
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Nov 22, 2020 RCV000559670.5
Benign 3 criteria provided, single submitter Apr 29, 2013 RCV000078466.9
Benign 1 criteria provided, single submitter Aug 7, 2018 RCV001719815.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NPC1 - - GRCh38
GRCh37
1038 1083

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Apr 29, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000110322.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Niemann-Pick disease type C1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000407881.3
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Nov 22, 2020)
criteria provided, single submitter
Method: clinical testing
Niemann-Pick disease type C1
Allele origin: germline
Invitae
Accession: SCV000650833.4
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Aug 07, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000513948.5
Submitted: (Sep 29, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 12955717)
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001808800.1
Submitted: (Aug 24, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001923602.1
Submitted: (Sep 23, 2021)
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
Identification of 58 novel mutations in Niemann-Pick disease type C: correlation with biochemical phenotype and importance of PTC1-like domains in NPC1. Park WD Human mutation 2003 PMID: 12955717
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=NPC1 - - - -

Text-mined citations for rs61731962...

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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 Nov 27, 2021