WDR83OS

WD repeat domain 83 opposite strand

Basic information

Region (hg38): 19:12668073-12669415

Previous symbols: [ "C19orf56" ]

Links

ENSG00000105583 ∙ NCBI:51398 ∙ OMIM:618474 ∙ HGNC:30203 ∙ Uniprot:Q9Y284 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with variable familial hypercholanemia	AR	Gastrointestinal	The condition can include pruritus and hepatic dysfunction, including hypercholanemia, and awareness may enable medical management	Craniofacial; Gastrointestinal; Musculoskeletal; Neurologic	30250217; 39471804

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WDR83OS gene.

• not_provided (18 variants)
• not_specified (8 variants)
• Hypercholanemia,_familial (5 variants)
• Neurodevelopmental_disorder_with_variable_familial_hypercholanemia (3 variants)
• Neurodevelopmental_disorder_with_seizures_and_speech_and_walking_impairment (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR83OS gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016145.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	5	1	7
missense			10	1		11
nonsense	2					2
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)	3	1				4
Total	5	1	12	6	1

Highest pathogenic variant AF is 0.0000041044386

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR83OS	protein_coding	protein_coding	ENST00000596731	4	3286

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00331	0.626	125722	0	12	125734	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.700	50	66.0	0.757	0.00000346	702
Missense in Polyphen		20	28.747	0.69573		314
Synonymous	0.214	25	26.4	0.947	0.00000156	178
Loss of Function	0.479	4	5.18	0.773	2.19e-7	60

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.000544	0.000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.118

Intolerance Scores

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.143
• hipred: N
• hipred_score: 0.454
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Wdr83os

Gene ontology

• Cellular component: integral component of membrane