NM_015910.7(WDPCP):c.1094A>G (p.Glu365Gly) AND Bardet-Biedl syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 16, 2022
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:: RCV000402624.8

Allele description [Variation Report for NM_015910.7(WDPCP):c.1094A>G (p.Glu365Gly)]

NM_015910.7(WDPCP):c.1094A>G (p.Glu365Gly)

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.1094A>G (p.Glu365Gly)

HGVS:

NC_000002.12:g.63404389T>C
NG_028144.2:g.441437A>G
NM_001042692.3:c.617A>G
NM_001354044.2:c.1022A>G
NM_001354045.2:c.1094A>G
NM_015910.7:c.1094A>GMANE SELECT
NP_001036157.1:p.Glu206Gly
NP_001340973.1:p.Glu341Gly
NP_001340974.1:p.Glu365Gly
NP_056994.3:p.Glu365Gly
NC_000002.11:g.63631524T>C
NM_015910.5:c.1094A>G
NR_122106.2:n.741A>G
NR_148704.2:n.1552A>G
NR_148705.2:n.1300A>G

Protein change:

E206G

Links:

dbSNP: rs201662623

NCBI 1000 Genomes Browser:

rs201662623

Molecular consequence:

NM_001042692.3:c.617A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354044.2:c.1022A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354045.2:c.1094A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015910.7:c.1094A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_122106.2:n.741A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148704.2:n.1552A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148705.2:n.1300A>G - 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
SCV001223278	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 16, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 27158779, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001223278

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 16, 2022)

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

The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery.

Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelly MR, Kim S, Park TJ, Braun DA, Pierquin G, Biver A, Wagner K, Malfroot A, Panigrahi I, Franco B, Al-Lami HA, Yeung Y, Choi YJ; University of Washington Center for Mendelian Genomics., et al.

Nat Genet. 2016 Jun;48(6):648-56. doi: 10.1038/ng.3558. Epub 2016 May 9. Erratum in: Nat Genet. 2016 Jul 27;48(8):970. doi: 10.1038/ng0816-970b.

PubMed [citation]

PMID:: 27158779
PMCID:: PMC4978421

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 Invitae, SCV001223278.4

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

Description

This sequence change replaces glutamic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 365 of the WDPCP protein (p.Glu365Gly). This variant is present in population databases (rs201662623, gnomAD 0.02%). This missense change has been observed in individual(s) with cerebellar vermis hypoplasia, ataxia and retinal dystrophy (PMID: 27158779). ClinVar contains an entry for this variant (Variation ID: 336766). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). 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.

#	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: May 26, 2024

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