NM_020779.4(WDR35):c.171_178del (p.Ser59fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 9, 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:: RCV003817878.2

Allele description [Variation Report for NM_020779.4(WDR35):c.171_178del (p.Ser59fs)]

NM_020779.4(WDR35):c.171_178del (p.Ser59fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p24.1

Genomic location:

Preferred name:

NM_020779.4(WDR35):c.171_178del (p.Ser59fs)

HGVS:

NC_000002.12:g.19982499_19982506del
NG_021212.1:g.12618_12625del
NM_001006657.2:c.171_178del
NM_020779.4:c.171_178delMANE SELECT
NP_001006658.1:p.Ser59fs
NP_065830.2:p.Ser59fs
NC_000002.11:g.20182260_20182267del

Protein change:

S59fs

Molecular consequence:

NM_001006657.2:c.171_178del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_020779.4:c.171_178del - frameshift variant - [Sequence Ontology: SO:0001589]

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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Streptomyces djakartensis JCM 4957 DNA, sequence099, whole genome shotgun sequen...
Streptomyces djakartensis JCM 4957 DNA, sequence099, whole genome shotgun sequence
gi|1903073443|dbj|BMWE01000099.1||g S:BMWE01|sequence099

Nucleotide
Microplana fuscomaculosa voucher PT778 internal transcribed spacer 1 and 5.8S ri...
Microplana fuscomaculosa voucher PT778 internal transcribed spacer 1 and 5.8S ribosomal RNA gene, partial sequence
gi|1007357496|gb|KU897062.1|

Nucleotide
Microplana nana voucher PT802 18S ribosomal RNA gene, partial sequence; internal...
Microplana nana voucher PT802 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, complete sequence; and 5.8S ribosomal RNA gene, partial sequence
gi|1007357498|gb|KU897064.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004607333	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 9, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 22486404, 29068549, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004607333

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 9, 2023)

germline

clinical testing

PubMed (3)
[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

Novel WDR35 mutations in patients with cranioectodermal dysplasia (Sensenbrenner syndrome).

Hoffer JL, Fryssira H, Konstantinidou AE, Ropers HH, Tzschach A.

Clin Genet. 2013 Jan;83(1):92-5. doi: 10.1111/j.1399-0004.2012.01880.x. Epub 2012 Apr 9. No abstract available.

PubMed [citation]

PMID:: 22486404

Expanding the genetic architecture and phenotypic spectrum in the skeletal ciliopathies.

Zhang W, Taylor SP, Ennis HA, Forlenza KN, Duran I, Li B, Sanchez JAO, Nevarez L, Nickerson DA, Bamshad M; University of Washington Center for Mendelian Genomics., Lachman RS, Krakow D, Cohn DH.

Hum Mutat. 2018 Jan;39(1):152-166. doi: 10.1002/humu.23362. Epub 2017 Nov 6.

PubMed [citation]

PMID:: 29068549
PMCID:: PMC6198324

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004607333.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Ser59Phefs*7) in the WDR35 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in WDR35 are known to be pathogenic (PMID: 22486404, 29068549). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with WDR35-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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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