WDR83

WD repeat domain 83, the group of Spliceosomal P complex|WD repeat domain containing|Spliceosomal C complex

Basic information

Region (hg38): 19:12666802-12675832

Links

ENSG00000123154 ∙ NCBI:84292 ∙ OMIM:616850 ∙ HGNC:32672 ∙ Uniprot:Q9BRX9 ∙ 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 WDR83 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR83 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						0
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			7	4	3	14
Total	0	0	28	5	3

Variants in WDR83

This is a list of pathogenic ClinVar variants found in the WDR83 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12668365-T-TG			Uncertain significance (Apr 29, 2023)
19-12668371-C-T			Likely benign (Nov 24, 2023)
19-12668409-C-T			Uncertain significance (Jun 25, 2023)
19-12668419-GGACAGCCTGA-G		Hypercholanemia, familial	Pathogenic (Aug 13, 2024)
19-12668435-G-C			Uncertain significance (Nov 27, 2023)
19-12668539-G-A		Hypercholanemia, familial	Pathogenic (Aug 13, 2024)
19-12668580-A-G		not specified	Uncertain significance (Jun 17, 2024)
19-12668636-G-A			Likely benign (Sep 27, 2022)
19-12669126-A-T		Hypercholanemia, familial	Pathogenic (Aug 13, 2024)
19-12669127-C-A		Neurodevelopmental disorder with seizures and speech and walking impairment • Hypercholanemia, familial	Conflicting classifications of pathogenicity (Aug 13, 2024)
19-12669169-G-A			Likely benign (Jan 03, 2024)
19-12669199-A-G			Benign (Nov 10, 2023)
19-12669345-G-C			Likely benign (Jul 14, 2023)
19-12669353-C-A		Hypercholanemia, familial	Pathogenic (Aug 13, 2024)
19-12669365-G-A			Benign (Jan 25, 2024)
19-12669382-C-G		not specified	Uncertain significance (Oct 06, 2021)
19-12669390-T-C			Benign (Jan 22, 2024)
19-12669396-G-C			Uncertain significance (May 27, 2022)
19-12669399-G-C		not specified	Uncertain significance (Apr 08, 2024)
19-12669849-C-T		not specified	Uncertain significance (Sep 16, 2021)
19-12669863-C-A		not specified	Uncertain significance (Jun 29, 2023)
19-12669899-C-T			Benign (May 08, 2018)
19-12669994-C-G		not specified	Uncertain significance (Oct 06, 2022)
19-12670214-G-A		not specified	Uncertain significance (Aug 09, 2021)
19-12670251-G-C		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR83	protein_coding	protein_coding	ENST00000418543	9	9033

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.45e-12	0.0343	125696	0	52	125748	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0978	189	193	0.980	0.0000111	1995
Missense in Polyphen		67	69.592	0.96275		736
Synonymous	0.457	80	85.4	0.937	0.00000476	648
Loss of Function	-0.0843	17	16.6	1.02	7.16e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000432	0.000420
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000109	0.000109
South Asian	0.000523	0.000523
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Molecular scaffold protein for various multimeric protein complexes. Acts as a module in the assembly of a multicomponent scaffold for the ERK pathway, linking ERK responses to specific agonists. At low concentrations it enhances ERK activation, whereas high concentrations lead to the inhibition of ERK activation. Also involved in response to hypoxia by acting as a negative regulator of HIF1A/HIF-1-alpha via its interaction with EGLN3/PHD3. May promote degradation of HIF1A. May act by recruiting signaling complexes to a specific upstream activator (By similarity). May also be involved in pre-mRNA splicing. {ECO:0000250}.
• Pathway: EGF-Ncore;MAP2K and MAPK activation;Signal Transduction;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades (Consensus)

Intolerance Scores

• loftool: 0.444
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.389
• ghis: 0.583

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr83
• Phenotype: homeostasis/metabolism phenotype; cellular 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); 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); renal/urinary system phenotype; immune system phenotype; embryo phenotype

Gene ontology

• Biological process: MAPK cascade;RNA splicing, via transesterification reactions;mRNA splicing, via spliceosome
• Cellular component: spliceosomal complex;endosome membrane;catalytic step 2 spliceosome
• Molecular function: protein binding