Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_003383.5(VLDLR):c.175G>A (p.Val59Ile)

Help
Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Aug 19, 2021)
Last evaluated:
Jan 12, 2018
Accession:
VCV000130705.3
Variation ID:
130705
Description:
single nucleotide variant
Help

NM_003383.5(VLDLR):c.175G>A (p.Val59Ile)

Allele ID
136151
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9p24.2
Genomic location
9: 2635545 (GRCh38) GRCh38 UCSC
9: 2635545 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.2635545G>A
NC_000009.12:g.2635545G>A
NM_003383.5:c.175G>A MANE Select NP_003374.3:p.Val59Ile missense
... more HGVS
Protein change
V59I
Other names
p.V59I:GTT>ATT
Canonical SPDI
NC_000009.12:2635544:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.07947 (A)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.05936
The Genome Aggregation Database (gnomAD), exomes 0.02405
1000 Genomes Project 0.07947
The Genome Aggregation Database (gnomAD) 0.05116
Exome Aggregation Consortium (ExAC) 0.02730
Links
ClinGen: CA155916
UniProtKB: P98155#VAR_011865
dbSNP: rs6149
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, single submitter Jan 31, 2014 RCV000118819.5
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000333724.1
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV001167940.1
Likely benign 1 no assertion criteria provided - RCV001573169.1
Help
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

Help
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: SCV000479334.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jan 31, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000169803.9
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
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Cerebellar ataxia, mental retardation, and dysequilibrium syndrome 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001330491.1
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
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000153466.2
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)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001798616.1
Submitted: (Aug 19, 2021)
Evidence details

Functional evidence

Help
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

Help
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 rs6149...

Help
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 Aug 25, 2021