WDR41

WD repeat domain 41, the group of WD repeat domain containing|SWC tripartite complex

Basic information

Region (hg38): 5:77425970-77620611

Links

ENSG00000164253 ∙ NCBI:55255 ∙ OMIM:617502 ∙ HGNC:25601 ∙ Uniprot:Q9HAD4 ∙ 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 WDR41 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR41 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			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in WDR41

This is a list of pathogenic ClinVar variants found in the WDR41 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-77426429-T-A			Likely benign (Dec 22, 2023)
5-77426455-T-G			Uncertain significance (Jul 21, 2022)
5-77426503-G-A			Likely benign (Jul 04, 2021)
5-77426518-A-G		Autosomal dominant striatal neurodegeneration type 1	Benign/Likely benign (Jan 13, 2024)
5-77426541-CATCT-C			Uncertain significance (Nov 05, 2022)
5-77426544-C-CT		Autosomal dominant striatal neurodegeneration type 1	Uncertain significance (Aug 20, 2019)
5-77426582-C-G		Autosomal dominant striatal neurodegeneration type 1	Uncertain significance (Jan 13, 2018)
5-77426584-G-A		Autosomal dominant striatal neurodegeneration type 1	Likely benign (Jan 12, 2018)
5-77426611-C-T		Autosomal dominant striatal neurodegeneration type 1	Benign (Jan 12, 2018)
5-77426617-C-T		Striatal Degeneration • Autosomal dominant striatal neurodegeneration type 1	Benign (Jan 12, 2018)
5-77426618-G-A		Striatal Degeneration • Autosomal dominant striatal neurodegeneration type 1	Benign (Jan 13, 2018)
5-77426624-C-T		Autosomal dominant striatal neurodegeneration type 1	Benign (Jan 13, 2018)
5-77426733-G-A		Autosomal dominant striatal neurodegeneration type 1	Uncertain significance (Jan 12, 2018)
5-77426841-C-T		Autosomal dominant striatal neurodegeneration type 1	Uncertain significance (Jan 13, 2018)
5-77426849-C-CT		Striatal Degeneration	Uncertain significance (Jun 14, 2016)
5-77426895-C-T		Autosomal dominant striatal neurodegeneration type 1	Benign (Jan 13, 2018)
5-77426990-C-T		Autosomal dominant striatal neurodegeneration type 1	Uncertain significance (Jan 13, 2018)
5-77426991-A-G		Autosomal dominant striatal neurodegeneration type 1	Benign (Jan 13, 2018)
5-77426993-C-T		Autosomal dominant striatal neurodegeneration type 1	Benign (Jan 13, 2018)
5-77426999-G-A		Autosomal dominant striatal neurodegeneration type 1	Uncertain significance (Jan 13, 2018)
5-77427010-A-G		Autosomal dominant striatal neurodegeneration type 1	Benign (Jan 13, 2018)
5-77427034-T-G		Autosomal dominant striatal neurodegeneration type 1	Benign (Jan 13, 2018)
5-77427039-G-GA		Striatal Degeneration	Benign (Jun 14, 2016)
5-77427050-A-G		Autosomal dominant striatal neurodegeneration type 1	Benign (Jan 12, 2018)
5-77427052-C-A		Autosomal dominant striatal neurodegeneration type 1	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR41	protein_coding	protein_coding	ENST00000296679	13	194642

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.50e-14	0.208	125556	0	192	125748	0.000764

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.165	245	238	1.03	0.0000115	2975
Missense in Polyphen		79	77.029	1.0256		955
Synonymous	0.474	83	88.7	0.936	0.00000445	875
Loss of Function	1.07	24	30.4	0.790	0.00000156	332

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00168	0.00168
Ashkenazi Jewish	0.000497	0.000496
East Asian	0.00104	0.00103
Finnish	0.000420	0.000370
European (Non-Finnish)	0.000805	0.000800
Middle Eastern	0.00104	0.00103
South Asian	0.000892	0.000882
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Non-catalytic component of the C9orf72-SMCR8 complex, a complex that has guanine nucleotide exchange factor (GEF) activity and regulates autophagy (PubMed:27193190, PubMed:27103069, PubMed:27617292, PubMed:28195531). The C9orf72-SMCR8 complex promotes the exchange of GDP to GTP, converting inactive GDP-bound RAB8A and RAB39B into their active GTP-bound form, thereby promoting autophagosome maturation (PubMed:27103069). The C9orf72- SMCR8 complex also acts as a negative regulator of autophagy initiation by interacting with the ATG1/ULK1 kinase complex and inhibiting its protein kinase activity (PubMed:27103069, PubMed:27617292). {ECO:0000269|PubMed:27103069, ECO:0000269|PubMed:27193190, ECO:0000269|PubMed:27617292, ECO:0000269|PubMed:28195531}.

Intolerance Scores

• loftool: 0.933
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.83

Haploinsufficiency Scores

• pHI: 0.466
• hipred: N
• hipred_score: 0.442
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.144

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr41

Gene ontology

• Biological process: autophagy;regulation of autophagy
• Cellular component: cytoplasm;lysosomal membrane;guanyl-nucleotide exchange factor complex;Atg1/ULK1 kinase complex
• Molecular function: protein binding;Rab guanyl-nucleotide exchange factor activity