NM_015910.7(WDPCP):c.2063A>G (p.Asn688Ser) AND not provided

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Jul 1, 2024
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:: RCV000514094.15

Allele description [Variation Report for NM_015910.7(WDPCP):c.2063A>G (p.Asn688Ser)]

NM_015910.7(WDPCP):c.2063A>G (p.Asn688Ser)

Gene:

WDPCP:WD repeat containing planar cell polarity effector [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p15

Genomic location:

Preferred name:

NM_015910.7(WDPCP):c.2063A>G (p.Asn688Ser)

HGVS:

NC_000002.12:g.63174685T>C
NG_028144.2:g.671141A>G
NM_001042692.3:c.1586A>G
NM_001354044.2:c.1991A>G
NM_015910.7:c.2063A>GMANE SELECT
NP_001036157.1:p.Asn529Ser
NP_001340973.1:p.Asn664Ser
NP_056994.3:p.Asn688Ser
NC_000002.11:g.63401820T>C
NM_015910.5:c.2063A>G
NR_122106.2:n.1706A>G
NR_148704.2:n.2517A>G
NR_148705.2:n.2166A>G

Protein change:

N529S

Links:

dbSNP: rs61734468

NCBI 1000 Genomes Browser:

rs61734468

Molecular consequence:

NM_001042692.3:c.1586A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354044.2:c.1991A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015910.7:c.2063A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_122106.2:n.1706A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148704.2:n.2517A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148705.2:n.2166A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000611015	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Aug 18, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004154913	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Jul 1, 2024)	germline	clinical testing	Citation Link,
SCV005256975	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000611015

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Aug 18, 2017)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004154913

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Benign
(Jul 1, 2024)

germline

clinical testing

Citation Link,

SCV005256975

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign

germline

not provided

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	8	not provided	not provided	not provided	not provided	clinical testing, not provided
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000611015.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	0.010624	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV004154913.10

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	8	not provided	not provided	clinical testing	not provided

Description

WDPCP: BP4, BS1, BS2

#	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		8	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005256975.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	PubMed (1)

#	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

Last Updated: Oct 20, 2024

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