WDR36

WD repeat domain 36, the group of UTPb subcomplex|WD repeat domain containing

Basic information

Region (hg38): 5:111092320-111130502

Previous symbols: [ "GLC1G" ]

Links

ENSG00000134987 ∙ NCBI:134430 ∙ OMIM:609669 ∙ HGNC:30696 ∙ Uniprot:Q8NI36 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• glaucoma 1, open angle, G (Limited), mode of inheritance: Unknown
• glaucoma 1, open angle, G (Disputed Evidence), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WDR36 gene.

• not provided (129 variants)
• Inborn genetic diseases (37 variants)
• Primary open angle glaucoma (14 variants)
• Glaucoma 1, open angle, G (12 variants)
• not specified (7 variants)
• WDR36-related condition (1 variants)
• Usher syndrome type 2C (1 variants)
• High myopia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR36 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				7	7	14
missense			51	4	3	58
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding			10	36	52	98
Total	0	0	63	47	62

Variants in WDR36

This is a list of pathogenic ClinVar variants found in the WDR36 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-111092339-G-A			Benign/Likely benign (Oct 04, 2022)
5-111092362-T-C			Benign (Sep 29, 2023)
5-111092379-C-A			Uncertain significance (Jun 27, 2022)
5-111092387-C-G		not specified • Primary open angle glaucoma	Conflicting classifications of pathogenicity (Dec 01, 2023)
5-111092395-A-C			Likely benign (Apr 14, 2023)
5-111092463-C-T		not specified	Uncertain significance (Aug 19, 2023)
5-111092482-C-A		not specified	Uncertain significance (May 27, 2022)
5-111092509-G-T		not specified	Uncertain significance (Apr 07, 2022)
5-111092511-G-C		not specified	Uncertain significance (Apr 07, 2022)
5-111092532-G-A		not specified	Uncertain significance (Jan 02, 2024)
5-111092544-G-T		not specified	Uncertain significance (Nov 07, 2023)
5-111092567-G-T		High myopia	Uncertain significance (Sep 12, 2022)
5-111092571-C-G			Uncertain significance (Sep 23, 2022)
5-111092610-A-G		not specified	Uncertain significance (Aug 28, 2023)
5-111092611-C-T		not specified	Uncertain significance (Feb 16, 2023)
5-111092614-A-T		not specified	Uncertain significance (May 24, 2023)
5-111094656-A-G			Benign (Jun 26, 2018)
5-111094907-C-CT		Primary open angle glaucoma • WDR36-related disorder	Benign/Likely benign (Jan 16, 2024)
5-111097096-G-A		not specified	Uncertain significance (Mar 29, 2016)
5-111097111-G-A		not specified	Uncertain significance (May 23, 2023)
5-111097112-C-T			Uncertain significance (Apr 19, 2022)
5-111097122-C-T		WDR36-related disorder	Benign (Jan 02, 2024)
5-111097143-T-C			Benign (Jan 15, 2024)
5-111097148-A-G			Uncertain significance (May 24, 2022)
5-111097388-A-G			Benign (Jun 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR36	protein_coding	protein_coding	ENST00000506538	23	38787

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000572	0.999	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.80	616	503	1.23	0.0000245	6212
Missense in Polyphen		156	158.27	0.98564		1997
Synonymous	-2.69	223	177	1.26	0.00000864	1844
Loss of Function	4.64	16	52.1	0.307	0.00000256	635

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000369	0.000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000711	0.0000703
Middle Eastern	0.000327	0.000326
South Asian	0.000230	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the nucleolar processing of SSU 18S rRNA. Involved in T-cell activation and highly coregulated with IL2. {ECO:0000269|PubMed:21051332}.
• Disease: DISEASE: Glaucoma 1, open angle, G (GLC1G) [MIM:609887]: A form of primary open angle glaucoma (POAG). POAG is characterized by a specific pattern of optic nerve and visual field defects. The angle of the anterior chamber of the eye is open, and usually the intraocular pressure is increased. However, glaucoma can occur at any intraocular pressure. The disease is generally asymptomatic until the late stages, by which time significant and irreversible optic nerve damage has already taken place. {ECO:0000269|PubMed:15677485, ECO:0000269|PubMed:18172102}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.439
• rvis_EVS: 0.03
• rvis_percentile_EVS: 55.86

Haploinsufficiency Scores

• pHI: 0.0995
• hipred: N
• hipred_score: 0.426
• ghis: 0.617

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.893

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr36
• 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); embryo phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: wdr36
• Affected structure: retinal ganglion cell
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

• Biological process: retina homeostasis;rRNA processing;visual perception;biological_process;regulation of axon extension;response to stimulus
• Cellular component: cellular_component;nucleoplasm;nucleolus;small-subunit processome;Pwp2p-containing subcomplex of 90S preribosome
• Molecular function: RNA binding