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NM_153026.3(PRICKLE1):c.370G>A (p.Ala124Thr)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000130027.7
Variation ID:
130027
Description:
single nucleotide variant
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NM_153026.3(PRICKLE1):c.370G>A (p.Ala124Thr)

Allele ID
135473
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q12
Genomic location
12: 42469464 (GRCh38) GRCh38 UCSC
12: 42863266 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.12:g.42469464C>T
Q96MT3:p.Ala124Thr
NC_000012.11:g.42863266C>T
... more HGVS
Protein change
A124T
Other names
p.A124T:GCT>ACT
NM_001144881.1(PRICKLE1):c.370G>A(p.Ala124Thr)
NM_001144882.1(PRICKLE1):c.370G>A(p.Ala124Thr)
NM_001144883.1(PRICKLE1):c.370G>A(p.Ala124Thr)
NM_153026.2(PRICKLE1):c.370G>A(p.Ala124Thr)
Canonical SPDI
NC_000012.12:42469463:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.02736 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.01351
The Genome Aggregation Database (gnomAD), exomes 0.01409
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00169
The Genome Aggregation Database (gnomAD) 0.00726
1000 Genomes Project 0.02736
Links
ClinGen: CA154769
UniProtKB: Q96MT3#VAR_066853
dbSNP: rs79087668
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 4 criteria provided, multiple submitters, no conflicts May 31, 2018 RCV000118053.5
Benign 1 criteria provided, single submitter Dec 8, 2020 RCV000313184.5
Benign 1 criteria provided, single submitter Feb 22, 2016 RCV000716761.1
Pathogenic 1 no assertion criteria provided Jan 1, 2017 RCV000656031.2
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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
375 389

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(May 31, 2018)
criteria provided, single submitter
Method: curation
Not specified
Allele origin: unknown
SIB Swiss Institute of Bioinformatics
Accession: SCV000803589.1
Submitted: (Jun 13, 2018)
Evidence details
Comment:
This variant is interpreted as a Benign - Stand Alone. The following ACMG Tag(s) were applied: BA1 => Allele frequency is >5% in Exome Sequencing … (more)
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Progressive myoclonus epilepsy with ataxia
Allele origin: germline
Invitae
Accession: SCV000561675.4
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Apr 12, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000171178.10
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
(Feb 22, 2016)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000847604.2
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
(Jul 02, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000230464.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
http://www.ncbi.nlm.nih.gov/vari…
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000152382.2
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)
Pathogenic
(Jan 01, 2017)
no assertion criteria provided
Method: case-control
Rolandic epilepsy
Allele origin: germline
Bioinformatics Core,Luxembourg Center for Systems Biomedicine
Study: EUROEPINOMICS COGIE
Accession: SCV000588307.1
Submitted: (Aug 09, 2017)
Evidence details
Publications
PubMed (1)
Comment:
CAADphred>15

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
Exome-wide analysis of mutational burden in patients with typical and atypical Rolandic epilepsy. Bobbili DR European journal of human genetics : EJHG 2018 PMID: 29358611
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PRICKLE1 - - - -
http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/?chr=12&from=42863266&to=42863266 - - - -

Text-mined citations for rs79087668...

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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