WDR26

WD repeat domain 26, the group of MicroRNA protein coding host genes|WD repeat domain containing

Basic information

Region (hg38): 1:224385146-224437033

Links

ENSG00000162923NCBI:80232OMIM:617424HGNC:21208Uniprot:Q9H7D7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Skraban-Deardorff syndrome (Strong), mode of inheritance: AD
  • Skraban-Deardorff syndrome (Strong), mode of inheritance: AD
  • Skraban-Deardorff syndrome (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Skraban-Deardorff syndromeADGeneralGenetic knowledge may potentially be beneficial related to manifestations such as renal issues; Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Dental; Musculoskeletal; Neurologic28686853

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WDR26 gene.

  • Skraban-Deardorff syndrome (13 variants)
  • not provided (11 variants)
  • Inborn genetic diseases (6 variants)
  • WDR26-related disorder (1 variants)
  • Intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR26 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
6
clinvar
4
clinvar
10
missense
10
clinvar
93
clinvar
8
clinvar
111
nonsense
7
clinvar
1
clinvar
8
start loss
0
frameshift
21
clinvar
1
clinvar
1
clinvar
23
inframe indel
1
clinvar
5
clinvar
4
clinvar
2
clinvar
12
splice donor/acceptor (+/-2bp)
4
clinvar
1
clinvar
5
splice region
4
1
5
non coding
2
clinvar
1
clinvar
2
clinvar
5
Total 32 14 101 19 8

Variants in WDR26

This is a list of pathogenic ClinVar variants found in the WDR26 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
1-224389854-C-A Inborn genetic diseases Uncertain significance (Oct 26, 2017)522069
1-224393839-T-C not specified Uncertain significance (Jan 05, 2023)2429289
1-224393839-TGGT-AACATTATACAAA WDR26-related disorder Uncertain significance (Jul 26, 2023)2631771
1-224393853-A-G WDR26-related disorder Likely benign (Apr 01, 2019)3059746
1-224393863-C-A Uncertain significance (Dec 18, 2023)3369984
1-224393884-T-C Skraban-Deardorff syndrome Pathogenic/Likely pathogenic (Jan 06, 2023)986836
1-224393906-T-C not specified Uncertain significance (Oct 22, 2018)1334865
1-224393949-T-C not specified Likely benign (Jun 07, 2024)3339684
1-224393959-G-A WDR26-related disorder Uncertain significance (Aug 03, 2023)2629411
1-224393979-T-C Benign (Dec 31, 2019)767752
1-224393994-C-T Inborn genetic diseases Pathogenic (Nov 19, 2018)985966
1-224398108-C-T not specified Uncertain significance (Sep 12, 2023)2627211
1-224398112-C-T Inborn genetic diseases Likely benign (Jan 08, 2022)2236451
1-224398124-C-T not specified Uncertain significance (Mar 01, 2024)3233698
1-224398141-C-A Uncertain significance (Jun 03, 2024)3384638
1-224398145-A-C Uncertain significance (Sep 06, 2022)2443503
1-224398195-ACT-A Skraban-Deardorff syndrome Pathogenic (Aug 05, 2024)801625
1-224398208-A-C Uncertain significance (Oct 01, 2020)1012763
1-224398228-T-C Pathogenic (Sep 01, 2024)3389651
1-224398256-A-C Skraban-Deardorff syndrome Benign (Dec 05, 2021)1684226
1-224398514-C-G Intellectual disability Pathogenic (Sep 10, 2020)981417
1-224398524-TACATTTAACA-T Inborn genetic diseases Pathogenic (Sep 22, 2017)522095
1-224398543-C-A Uncertain significance (Jan 01, 2023)1711239
1-224398543-C-T Skraban-Deardorff syndrome Uncertain significance (Sep 13, 2019)996856
1-224398548-A-AT Pathogenic (Oct 23, 2020)987180

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
WDR26protein_codingprotein_codingENST00000414423 1451891
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000003681255680101255780.0000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.581693610.4690.00001934291
Missense in Polyphen1790.640.187551027
Synonymous1.381171380.8500.000007131313
Loss of Function5.48035.00.000.00000183412

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.0003270.000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: G-beta-like protein involved in cell signal transduction (PubMed:15378603, PubMed:19446606, PubMed:22065575, PubMed:23625927, PubMed:27098453, PubMed:26895380). Acts as a negative regulator in MAPK signaling pathway (PubMed:15378603). Functions as a scaffolding protein to promote G beta:gamma- mediated PLCB2 plasma membrane translocation and subsequent activation in leukocytes (PubMed:22065575, PubMed:23625927). Core component of the CTLH E3 ubiquitin-protein ligase complex that selectively accepts ubiquitin from UBE2H and mediates ubiquitination and subsequent proteasomal degradation of the transcription factor HBP1 (PubMed:29911972). Acts as a negative regulator of the canonical Wnt signaling pathway through preventing ubiquitination of beta-catenin CTNNB1 by the beta- catenin destruction complex, thus negatively regulating CTNNB1 degradation (PubMed:27098453). Serves as a scaffold to coordinate PI3K/AKT pathway-driven cell growth and migration (PubMed:26895380). Protects cells from oxidative stress-induced apoptosis via the down-regulation of AP-1 transcriptional activity as well as by inhibiting cytochrome c release from mitochondria (PubMed:19446606). Protects also cells by promoting hypoxia- mediated autophagy and mitophagy (By similarity). {ECO:0000250|UniProtKB:F1LTR1, ECO:0000269|PubMed:15378603, ECO:0000269|PubMed:19446606, ECO:0000269|PubMed:23625927, ECO:0000269|PubMed:26895380, ECO:0000269|PubMed:27098453, ECO:0000269|PubMed:29911972}.;
Disease
DISEASE: Skraban-Deardorff syndrome (SKDEAS) [MIM:617616]: An autosomal dominant syndrome characterized by psychomotor developmental delay, intellectual disability with delayed speech, febrile and non-febrile seizures, abnormal gait, and facial dysmorphism. Facial features include a prominent maxilla and upper lip that readily reveal the upper gingiva, widely spaced teeth, and a broad nasal tip. {ECO:0000269|PubMed:28686853}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.156

Intolerance Scores

loftool
rvis_EVS
-0.47
rvis_percentile_EVS
23.04

Haploinsufficiency Scores

pHI
0.946
hipred
Y
hipred_score
0.673
ghis
0.614

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
K
gene_indispensability_pred
E
gene_indispensability_score
0.662

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Wdr26
Phenotype

Gene ontology

Biological process
Cellular component
ubiquitin ligase complex;nucleus;nucleoplasm;cytoplasm;mitochondrion;cytosol
Molecular function
protein binding