NM_001384732.1(CPLANE1):c.9169T>G (p.Cys3057Gly) AND multiple conditions

delete

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 6, 2018
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:: RCV000796630.1

Allele description

NM_001384732.1(CPLANE1):c.9169T>G (p.Cys3057Gly)

Gene:

CPLANE1:ciliogenesis and planar polarity effector complex subunit 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5p13.2

Genomic location:

Preferred name:

NM_001384732.1(CPLANE1):c.9169T>G (p.Cys3057Gly)

HGVS:

NC_000005.10:g.37121633A>C
NG_032772.2:g.132796T>G
NM_001384732.1:c.9169T>GMANE SELECT
NM_023073.4:c.9007T>G
NP_001371661.1:p.Cys3057Gly
NP_075561.3:p.Cys3003Gly
NP_075561.3:p.Cys3003Gly
NC_000005.9:g.37121735A>C
NM_023073.3:c.9007T>G

Protein change:

C3003G

Links:

dbSNP: rs760027584

NCBI 1000 Genomes Browser:

rs760027584

Molecular consequence:

NM_001384732.1:c.9169T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_023073.4:c.9007T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Orofaciodigital syndrome type 6 (OFD6)
Synonyms:: OFDS VI; POLYDACTYLY, CLEFT LIP/PALATE OR LINGUAL LUMP, AND PSYCHOMOTOR RETARDATION; VARADI SYNDROME; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010176; MedGen: C2745997; Orphanet: 2754; OMIM: 277170

Name:: Joubert syndrome 17 (JBTS17)
Identifiers:: MONDO: MONDO:0013824; MedGen: C3553264; Orphanet: 475; OMIM: 614615

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000936151	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 6, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000936151

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 6, 2018)

germline

clinical testing

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000936151.1

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

Description

This sequence change replaces cysteine with glycine at codon 3003 of the C5orf42 protein (p.Cys3003Gly). The cysteine residue is weakly conserved and there is a large physicochemical difference between cysteine and glycine. This variant is present in population databases (rs760027584, ExAC 0.02%). This variant has not been reported in the literature in individuals with C5orf42-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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: Feb 7, 2023

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