NM_015910.7(WDPCP):c.1798C>T (p.Arg600Cys) AND Bardet-Biedl syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 25, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001904997.6

Allele description [Variation Report for NM_015910.7(WDPCP):c.1798C>T (p.Arg600Cys)]

NM_015910.7(WDPCP):c.1798C>T (p.Arg600Cys)

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.1798C>T (p.Arg600Cys)

HGVS:

NC_000002.12:g.63313262G>A
NG_028144.2:g.532564C>T
NM_001042692.3:c.1321C>T
NM_001354044.2:c.1726C>T
NM_015910.7:c.1798C>TMANE SELECT
NP_001036157.1:p.Arg441Cys
NP_001340973.1:p.Arg576Cys
NP_056994.3:p.Arg600Cys
NC_000002.11:g.63540397G>A
NR_122106.2:n.1445C>T
NR_148704.2:n.2256C>T
NR_148705.2:n.2004C>T

Protein change:

R441C

Links:

dbSNP: rs747517141

NCBI 1000 Genomes Browser:

rs747517141

Molecular consequence:

NM_001042692.3:c.1321C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354044.2:c.1726C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_015910.7:c.1798C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_122106.2:n.1445C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148704.2:n.2256C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148705.2:n.2004C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Bardet-Biedl syndrome (BBS)
Identifiers:: MONDO: MONDO:0015229; MedGen: C0752166; Orphanet: 110; OMIM: PS209900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002134649	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 25, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 32483926, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002134649

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 25, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Comprehensive genomic diagnosis of inherited retinal and optical nerve disorders reveals hidden syndromes and personalized therapeutic options.

Diñeiro M, Capín R, Cifuentes GÁ, Fernández-Vega B, Villota E, Otero A, Santiago A, Pruneda PC, Castillo D, Viejo-Díaz M, Hernando I, Durán NS, Álvarez R, Lago CG, Ordóñez GR, Fernández-Vega Á, Cabanillas R, Cadiñanos J.

Acta Ophthalmol. 2020 Dec;98(8):e1034-e1048. doi: 10.1111/aos.14479. Epub 2020 Jun 1.

PubMed [citation]

PMID:: 32483926
PMCID:: PMC7754416

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002134649.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt WDPCP protein function. ClinVar contains an entry for this variant (Variation ID: 1363607). This missense change has been observed in individual(s) with inherited retinal disease (PMID: 32483926). This variant is present in population databases (rs747517141, gnomAD 0.003%). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 600 of the WDPCP protein (p.Arg600Cys).

#	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: Dec 28, 2024

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