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NM_000271.5(NPC1):c.3598A>G (p.Ser1200Gly)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(4);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Sep 30, 2021)
Last evaluated:
Dec 6, 2020
Accession:
VCV000284662.8
Variation ID:
284662
Description:
single nucleotide variant
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NM_000271.5(NPC1):c.3598A>G (p.Ser1200Gly)

Allele ID
268899
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
18q11.2
Genomic location
18: 23533511 (GRCh38) GRCh38 UCSC
18: 21113475 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000018.10:g.23533511T>C
NC_000018.9:g.21113475T>C
NG_012795.1:g.58107A>G
... more HGVS
Protein change
S1200G
Other names
-
Canonical SPDI
NC_000018.10:23533510:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00260 (C)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00088
Exome Aggregation Consortium (ExAC) 0.00097
Trans-Omics for Precision Medicine (TOPMed) 0.00366
The Genome Aggregation Database (gnomAD) 0.00388
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00469
1000 Genomes Project 0.00260
Links
ClinGen: CA8912692
dbSNP: rs35248744
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Dec 6, 2020 RCV000611612.4
Benign 2 criteria provided, single submitter Nov 12, 2015 RCV000279532.5
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Apr 2, 2020 RCV000675554.5
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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 02, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000730592.2
Submitted: (Sep 30, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 23773996, 25764212, 30556376)
Benign
(Jun 30, 2017)
criteria provided, single submitter
Method: clinical testing
Niemann-Pick disease type C1
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Study: VKGL Data-share Consensus
Accession: SCV000744738.1
Submitted: (Apr 09, 2018)
Evidence details
Benign
(Nov 12, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000337368.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Feb 13, 2020)
criteria provided, single submitter
Method: clinical testing
Not provided
Allele origin: germline
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000801245.2
Submitted: (May 28, 2021)
Evidence details
Benign
(Dec 06, 2020)
criteria provided, single submitter
Method: clinical testing
Niemann-Pick disease type C1
Allele origin: germline
Invitae
Accession: SCV001012901.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
Niemann-Pick disease type C1
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV000733751.1
Submitted: (Apr 04, 2018)
Evidence details
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: SCV001807817.1
Submitted: (Aug 24, 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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=NPC1 - - - -

Text-mined citations for rs35248744...

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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 Oct 06, 2021