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NM_003383.5(VLDLR):c.468C>T (p.Pro156=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Feb 20, 2020)
Last evaluated:
Dec 31, 2019
Accession:
VCV000130712.4
Variation ID:
130712
Description:
single nucleotide variant
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NM_003383.5(VLDLR):c.468C>T (p.Pro156=)

Allele ID
136158
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9p24.2
Genomic location
9: 2643179 (GRCh38) GRCh38 UCSC
9: 2643179 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.12:g.2643179C>T
NC_000009.11:g.2643179C>T
NM_003383.5:c.468C>T MANE Select NP_003374.3:p.Pro156= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000009.12:2643178:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00399 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00086
The Genome Aggregation Database (gnomAD), exomes 0.00189
Trans-Omics for Precision Medicine (TOPMed) 0.00152
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Exome Aggregation Consortium (ExAC) 0.00188
1000 Genomes Project 0.00399
Links
ClinGen: CA155927
dbSNP: rs2242105
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, single submitter Aug 2, 2017 RCV000118826.5
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000261481.1
Benign 1 criteria provided, single submitter Dec 31, 2019 RCV000895969.2
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV001169797.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
VLDLR - - GRCh38
GRCh37
230 447

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Cerebellar Hypoplasia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000479336.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Aug 02, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000730491.1
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001040038.2
Submitted: (Jan 29, 2020)
Evidence details
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Cerebellar ataxia, mental retardation, and dysequilibrium syndrome 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001332573.1
Submitted: (Feb 20, 2020)
Evidence details
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)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000153473.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs2242105...

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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 Jun 14, 2021