WDR1

WD repeat domain 1, the group of MicroRNA protein coding host genes|WD repeat domain containing

Basic information

Region (hg38): 4:10068088-10116972

Links

ENSG00000071127 ∙ NCBI:9948 ∙ OMIM:604734 ∙ HGNC:12754 ∙ Uniprot:O75083 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WDR1 gene.

• not provided (360 variants)
• Inborn genetic diseases (27 variants)
• not specified (13 variants)
• Lazy leukocyte syndrome (3 variants)
• WDR1-related condition (3 variants)
• WDR1 deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR1 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			4	132	4	140
missense			111	4	3	118
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			10	19	2	31
non coding			1	76	18	95
Total	0	0	119	212	25

Variants in WDR1

This is a list of pathogenic ClinVar variants found in the WDR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-10072573-G-A		Intellectual developmental disorder 61	Pathogenic (Dec 14, 2020)
4-10075379-C-T			Likely benign (Jun 13, 2023)
4-10075391-G-A		Inborn genetic diseases	Uncertain significance (May 30, 2022)
4-10075402-G-C			Likely benign (Jan 06, 2022)
4-10075404-C-G		Inborn genetic diseases	Uncertain significance (Aug 17, 2021)
4-10075417-G-A			Likely benign (Apr 10, 2022)
4-10075423-C-A			Likely benign (Oct 05, 2022)
4-10075423-C-T			Likely benign (Jun 28, 2022)
4-10075426-G-A			Likely benign (May 24, 2022)
4-10075432-C-T			Likely benign (Oct 20, 2023)
4-10075437-G-T			Uncertain significance (Jun 04, 2022)
4-10075440-C-T		Inborn genetic diseases	Uncertain significance (Jan 26, 2023)
4-10075441-G-A			Likely benign (Dec 14, 2023)
4-10075484-T-A		Lazy leukocyte syndrome	Pathogenic (Jul 29, 2020)
4-10075491-A-C			Likely benign (Jan 29, 2024)
4-10075496-G-A			Likely benign (Nov 13, 2023)
4-10075496-G-T			Likely benign (Aug 04, 2023)
4-10075498-G-A			Likely benign (Aug 17, 2023)
4-10075502-A-G			Likely benign (Nov 23, 2022)
4-10077288-TG-T			Benign (Nov 09, 2023)
4-10077294-C-T			Likely benign (May 30, 2023)
4-10077294-CG-C			Likely benign (Apr 12, 2022)
4-10077295-G-A			Likely benign (Aug 17, 2022)
4-10077296-G-A			Benign (Nov 12, 2022)
4-10077326-C-T			Likely benign (Apr 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR1	protein_coding	protein_coding	ENST00000499869	15	42611

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00108	124626	0	2	124628	0.00000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.93	275	381	0.721	0.0000240	3967
Missense in Polyphen		71	142.62	0.49782		1569
Synonymous	-2.45	215	174	1.24	0.0000137	1149
Loss of Function	4.61	2	28.6	0.0699	0.00000131	342

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Induces disassembly of actin filaments in conjunction with ADF/cofilin family proteins (PubMed:15629458). Enhances cofilin-mediated actin severing (By similarity). Involved in cytokinesis. Involved in chemotactic cell migration by restricting lamellipodial membrane protrusions (PubMed:18494608). Involved in myocardium sarcomere organization. Required for cardiomyocyte growth and maintenance (By similarity). Involved in megakaryocyte maturation and platelet shedding. Required for the establishment of planar cell polarity (PCP) during follicular epithelium development and for cell shape changes during PCP; the function seems to implicate cooperation with CFL1 and/or DSTN/ADF. Involved in the generation/maintenance of cortical tension (By similarity). Involved in assembly and maintenance of epithelial apical cell junctions and plays a role in the organization of the perijunctional actomyosin belt (PubMed:25792565). {ECO:0000250|UniProtKB:O88342, ECO:0000250|UniProtKB:Q9W7F2, ECO:0000269|PubMed:15629458, ECO:0000269|PubMed:18494608, ECO:0000269|PubMed:25792565}.
• Pathway: Hypertrophy Model;TCR;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• rvis_EVS: -0.57
• rvis_percentile_EVS: 18.9

Haploinsufficiency Scores

• pHI: 0.629
• hipred: Y
• hipred_score: 0.662
• ghis: 0.645

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.944

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Wdr1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; hearing/vestibular/ear phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: wdr1
• Affected structure: mandibular arch skeleton
• Phenotype tag: abnormal
• Phenotype quality: protruding

Gene ontology

• Biological process: neutrophil mediated immunity;platelet degranulation;sensory perception of sound;regulation of cell shape;actin filament depolymerization;actin filament fragmentation;platelet formation;regulation of actin filament depolymerization;positive regulation of actin filament depolymerization;cortical cytoskeleton organization;locomotion;establishment of planar polarity of follicular epithelium;apical junction assembly;maintenance of epithelial cell apical/basal polarity;sarcomere organization;regulation of oligodendrocyte differentiation;regulation of ventricular cardiac muscle cell membrane repolarization;neutrophil migration
• Cellular component: podosome;extracellular region;cytosol;plasma membrane;cell-cell junction;cell junction;cortical actin cytoskeleton;actomyosin, actin portion;cell projection;myelin sheath;extracellular exosome
• Molecular function: actin filament binding