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NM_153026.3(PRICKLE1):c.1899T>C (p.Phe633=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 23, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000130024.11
Variation ID:
130024
Description:
single nucleotide variant
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NM_153026.3(PRICKLE1):c.1899T>C (p.Phe633=)

Allele ID
135470
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q12
Genomic location
12: 42460406 (GRCh38) GRCh38 UCSC
12: 42854208 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.42854208A>G
NC_000012.12:g.42460406A>G
NG_012965.1:g.134365T>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000012.12:42460405:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.27057 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.31757
The Genome Aggregation Database (gnomAD) 0.32044
The Genome Aggregation Database (gnomAD) 0.33283
The Genome Aggregation Database (gnomAD), exomes 0.34909
Exome Aggregation Consortium (ExAC) 0.34591
1000 Genomes Project 0.27057
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.29986
Trans-Omics for Precision Medicine (TOPMed) 0.31991
Links
ClinGen: CA154765
dbSNP: rs3747563
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, multiple submitters, no conflicts May 7, 2018 RCV000712845.4
Benign 4 criteria provided, single submitter Jul 2, 2014 RCV000118050.9
Benign 1 criteria provided, single submitter Jan 8, 2016 RCV000715151.1
Benign 1 criteria provided, single submitter Dec 5, 2020 RCV001517090.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PRICKLE1 - - GRCh38
GRCh37
379 393

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jul 02, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000232795.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(May 07, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000843383.1
Submitted: (Aug 31, 2018)
Evidence details
Benign
(Jan 08, 2016)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000845979.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA … (more)
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Progressive myoclonus epilepsy with ataxia
Allele origin: germline
Invitae
Accession: SCV001725504.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001889555.1
Submitted: (Sep 17, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000152378.2
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)
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001742837.3
Submitted: (Sep 02, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001929121.1
Submitted: (Sep 23, 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=PRICKLE1 - - - -

Text-mined citations for rs3747563...

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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