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NM_021222.3(PRUNE1):c.520G>T (p.Gly174Ter)

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, single submitter
Submissions:
2 (Most recent: May 22, 2017)
Accession:
VCV000402132.2
Variation ID:
402132
Description:
single nucleotide variant
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NM_021222.3(PRUNE1):c.520G>T (p.Gly174Ter)

Allele ID
389108
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q21.3
Genomic location
1: 151024795 (GRCh38) GRCh38 UCSC
1: 150997271 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.150997271G>T
NC_000001.11:g.151024795G>T
NG_052875.1:g.21405G>T
... more HGVS
Protein change
G174*
Other names
-
Canonical SPDI
NC_000001.11:151024794:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (C)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD) 0.00006
Links
ClinGen: CA16609498
OMIM: 617413.0004
dbSNP: rs200618384
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter - RCV000454323.1
Pathogenic 1 no assertion criteria provided Sep 19, 2017 RCV000490537.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PRUNE1 - - GRCh38
GRCh37
21 33

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(-)
criteria provided, single submitter
Method: research
Abnormality of brain morphology
(Autosomal recessive inheritance)
Allele origin: inherited
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine
Accession: SCV000537909.1
Submitted: (Mar 29, 2017)
Evidence details
Publications
PubMed (1)
Comment:
There are 3 more families with similar phenotype
Pathogenic
(Sep 19, 2017)
no assertion criteria provided
Method: literature only
NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, HYPOTONIA, AND VARIABLE BRAIN ANOMALIES
Allele origin: germline
OMIM
Accession: SCV000577904.2
Submitted: (May 22, 2017)
Evidence details
Publications
PubMed (1)

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
Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease. Karaca E Neuron 2015 PMID: 26539891

Text-mined citations for rs200618384...

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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 Sep 29, 2021