NM_020779.4(WDR35):c.3439T>C (p.Cys1147Arg) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 26, 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:: RCV002974863.3

Allele description [Variation Report for NM_020779.4(WDR35):c.3439T>C (p.Cys1147Arg)]

NM_020779.4(WDR35):c.3439T>C (p.Cys1147Arg)

Gene:

WDR35:WD repeat domain 35 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p24.1

Genomic location:

Preferred name:

NM_020779.4(WDR35):c.3439T>C (p.Cys1147Arg)

HGVS:

NC_000002.12:g.19913632A>G
NG_021212.1:g.81492T>C
NM_001006657.2:c.3472T>C
NM_020779.4:c.3439T>CMANE SELECT
NP_001006658.1:p.Cys1158Arg
NP_065830.2:p.Cys1147Arg
NC_000002.11:g.20113393A>G

Protein change:

C1147R

Molecular consequence:

NM_001006657.2:c.3472T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_020779.4:c.3439T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cranioectodermal dysplasia 2 (CED2)
Identifiers:: MONDO: MONDO:0013323; MedGen: C3150874; Orphanet: 1515; OMIM: 613610

Name:: Short-rib thoracic dysplasia 7 with or without polydactyly (SRTD7)
Synonyms:: Short rib polydactyly syndrome 5; SHORT-RIB THORACIC DYSPLASIA 7 WITH POLYDACTYLY
Identifiers:: MONDO: MONDO:0013569; MedGen: C3279792; Orphanet: 93271; OMIM: 614091

Recent activity

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centrosomal protein of 72 kDa [Vicugna pacos]
centrosomal protein of 72 kDa [Vicugna pacos]
gi|1777465148|ref|XP_031532771.1|

Protein
pachytene checkpoint protein 2 homolog isoform X4 [Vicugna pacos]
pachytene checkpoint protein 2 homolog isoform X4 [Vicugna pacos]
gi|1777465142|ref|XP_031532768.1|

Protein
Bergenia crassifolia WK23-ABG000163 maturase K (matK) gene, partial cds; chlorop...
Bergenia crassifolia WK23-ABG000163 maturase K (matK) gene, partial cds; chloroplast
gi|2618954009|gb|OR738292.1|

Nucleotide
Cercopithecus wolfi wolfi isolate CWW-1 NPAS3.2 gene, partial sequence
Cercopithecus wolfi wolfi isolate CWW-1 NPAS3.2 gene, partial sequence
gi|302453891|gb|HM759949.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003281720	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 26, 2022)	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

SCV003281720

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 26, 2022)

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003281720.2

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

Description

This variant is present in population databases (rs760064395, gnomAD 0.004%). This sequence change replaces cysteine, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 1158 of the WDR35 protein (p.Cys1158Arg). This variant has not been reported in the literature in individuals affected with WDR35-related conditions. 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 C0"). 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: Sep 29, 2024

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