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NM_000271.5(NPC1):c.688_693del (p.Ser230_Val231del)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Pathogenic(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 8, 2020
Accession:
VCV000290134.4
Variation ID:
290134
Description:
6bp deletion
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NM_000271.5(NPC1):c.688_693del (p.Ser230_Val231del)

Allele ID
274371
Variant type
Deletion
Variant length
6 bp
Cytogenetic location
18q11.2
Genomic location
18: 23560419-23560424 (GRCh38) GRCh38 UCSC
18: 21140383-21140388 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_000271.4:c.688_693delTCTGTG
NM_000271.4:c.688_693del
NC_000018.10:g.23560420_23560425del
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000018.10:23560418:CACAGAC:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA8913664
dbSNP: rs758687942
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Apr 28, 2017 RCV000492895.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Sep 8, 2020 RCV000669390.3
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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
Uncertain significance
(Sep 15, 2017)
criteria provided, single submitter
Method: clinical testing
Niemann-Pick disease type C1
Allele origin: unknown
Counsyl
Accession: SCV000794138.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (3)
Uncertain significance
(Aug 09, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000344636.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000581824.4
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The c.688_693delTCTGTG variant has been reported previously in association with Niemann-Pickdisease, type C (NPC) in patients who also harbored a second variant in the NPC1 … (more)
Likely pathogenic
(Sep 08, 2020)
criteria provided, single submitter
Method: clinical testing
Niemann-Pick disease type C1
Allele origin: germline
Invitae
Accession: SCV001410264.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This variant, c.688_693del, results in the deletion of 2 amino acid(s) of the NPC1 protein (p.Ser230_Val231del), but otherwise preserves the integrity of the reading frame. … (more)

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
Observational cohort study of the natural history of Niemann-Pick disease type C in the UK: a 5-year update from the UK clinical database. Imrie J BMC neurology 2015 PMID: 26666848
The National Niemann-Pick Type C1 Disease Database: correlation of lipid profiles, mutations, and biochemical phenotypes. Garver WS Journal of lipid research 2010 PMID: 19744920
Niemann-Pick C variant detection by altered sphingolipid trafficking and correlation with mutations within a specific domain of NPC1. Sun X American journal of human genetics 2001 PMID: 11349231
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=NPC1 - - - -

Text-mined citations for rs758687942...

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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