NM_153026.3(PRICKLE1):c.374T>C (p.Val125Ala) AND not specified

Germline classification:: Benign (4 submissions)
Last evaluated:: May 6, 2016
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000118054.24

Allele description [Variation Report for NM_153026.3(PRICKLE1):c.374T>C (p.Val125Ala)]

NM_153026.3(PRICKLE1):c.374T>C (p.Val125Ala)

Gene:

PRICKLE1:prickle planar cell polarity protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q12

Genomic location:

Preferred name:

NM_153026.3(PRICKLE1):c.374T>C (p.Val125Ala)

Other names:

p.V125A:GTG>GCG

HGVS:

NC_000012.12:g.42469460A>G
NG_012965.1:g.125311T>C
NM_001144881.2:c.374T>C
NM_001144882.2:c.374T>C
NM_001144883.2:c.374T>C
NM_153026.3:c.374T>CMANE SELECT
NP_001138353.1:p.Val125Ala
NP_001138354.1:p.Val125Ala
NP_001138355.1:p.Val125Ala
NP_694571.2:p.Val125Ala
NC_000012.11:g.42863262A>G
NM_153026.2:c.374T>C

Protein change:

V125A

Links:

dbSNP: rs34837068

NCBI 1000 Genomes Browser:

rs34837068

Molecular consequence:

NM_001144881.2:c.374T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001144882.2:c.374T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001144883.2:c.374T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_153026.3:c.374T>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000152383	Genetic Services Laboratory, University of Chicago	no assertion criteria provided	Likely benign	germline	clinical testing
SCV000171179	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Apr 8, 2014)	germline	clinical testing	Citation Link,
SCV000203341	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (Feb 28, 2014)	germline	clinical testing	Citation Link,
SCV000846552	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Benign (May 6, 2016)	germline	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000152383.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

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 disease phenotype. NOT Sanger confirmed.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV000171179.12

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

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 a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Eurofins Ntd Llc (ga), SCV000203341.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		1	not provided	not provided	not provided

From Ambry Genetics, SCV000846552.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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