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NM_153026.3(PRICKLE1):c.2304C>G (p.Ser768=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000096507.7
Variation ID:
96507
Description:
single nucleotide variant
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NM_153026.3(PRICKLE1):c.2304C>G (p.Ser768=)

Allele ID
102401
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q12
Genomic location
12: 42460001 (GRCh38) GRCh38 UCSC
12: 42853803 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.42853803G>C
NC_000012.12:g.42460001G>C
NM_153026.3:c.2304C>G MANE Select NP_694571.2:p.Ser768= synonymous
... more HGVS
Protein change
-
Other names
p.S768S:TCC>TCG
Canonical SPDI
NC_000012.12:42460000:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00599 (C)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00567
The Genome Aggregation Database (gnomAD) 0.00481
The Genome Aggregation Database (gnomAD), exomes 0.00145
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00646
Exome Aggregation Consortium (ExAC) 0.00184
1000 Genomes Project 0.00599
Links
ClinGen: CA285797
dbSNP: rs35854729
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 Jul 5, 2013 RCV000082659.6
Benign 1 criteria provided, single submitter Dec 8, 2020 RCV000363709.7
Likely benign 1 criteria provided, single submitter Mar 13, 2016 RCV000716961.1
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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
377 391

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jan 16, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000171189.12
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)
Likely benign
(Mar 13, 2016)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000847806.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign) ;Synonymous alterations with insufficient evidence to classify as benign
Benign
(Jul 05, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000114701.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Progressive myoclonus epilepsy with ataxia
Allele origin: germline
Invitae
Accession: SCV000561680.6
Submitted: (Jan 07, 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 rs35854729...

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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