chr2-19935522-T-A

Variant names:

• chr2-19935522-T-A
• rs6741091
• NM_001006657.2:c.2529A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001006657.2(WDR35):​c.2529A>T​(p.Glu843Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Synonymous variant affecting the same amino acid position (i.e. E843E) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: WDR35 NM_001006657.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 17 publications found

Genes affected

WDR35 (HGNC:29250): (WD repeat domain 35) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. Two patients with Sensenbrenner syndrome / cranioectodermal dysplasia (CED) were identified with mutations in this gene, consistent with a possible ciliary function.[provided by RefSeq, Sep 2010]

WDR35 Gene-Disease associations (from GenCC):

• cranioectodermal dysplasia 2

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, PanelApp Australia, ClinGen, Ambry Genetics
• short-rib thoracic dysplasia 7 with or without polydactyly

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet, Labcorp Genetics (formerly Invitae)
• cranioectodermal dysplasia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• short rib-polydactyly syndrome, Verma-Naumoff type

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.02547142).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR35	NM_001006657.2	c.2529A>T	p.Glu843Asp	missense_variant	Exon 22 of 28	ENST00000345530.8	NP_001006658.1
WDR35	NM_020779.4	c.2496A>T	p.Glu832Asp	missense_variant	Exon 21 of 27	ENST00000281405.9	NP_065830.2
WDR35	XM_011533007.3	c.1224A>T	p.Glu408Asp	missense_variant	Exon 11 of 17		XP_011531309.1
WDR35	XR_426989.4	n.2586A>T		non_coding_transcript_exon_variant	Exon 21 of 25

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR35	ENST00000345530.8	c.2529A>T	p.Glu843Asp	missense_variant	Exon 22 of 28	1	NM_001006657.2	ENSP00000314444.5
WDR35	ENST00000281405.9	c.2496A>T	p.Glu832Asp	missense_variant	Exon 21 of 27	1	NM_020779.4	ENSP00000281405.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 41

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 40185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.079
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.48
CADD	Benign	0.10
DANN	Benign	0.51
DEOGEN2	Benign	0.011	.;T;.
Eigen	Benign	-1.7
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.043	N
LIST_S2	Benign	0.73	T;T;T
M_CAP	Uncertain	0.11	D
MetaRNN	Benign	0.025	T;T;T
MetaSVM	Benign	-0.79	T
MutationAssessor	Benign	0.14	.;N;.
PhyloP100		-1.7
PrimateAI	Benign	0.35	T
PROVEAN	Benign	-0.24	N;N;N
REVEL	Benign	0.039
Sift	Benign	0.68	T;T;T
Sift4G	Benign	0.71	T;T;T
Polyphen		0.0010	B;B;.
Vest4		0.058
MutPred		0.31		.;Gain of helix (P = 0.0696);.;
MVP		0.23
MPC		0.11
ClinPred		0.032	T
GERP RS		-4.0
Varity_R		0.026
gMVP		0.14
Mutation Taster		=91/9	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6741091; hg19: chr2-20135283;