WDR45B

WD repeat domain 45B, the group of WD repeat domain containing|WIPI family

Basic information

Region (hg38): 17:82614561-82648553

Previous symbols: [ "WDR45L" ]

Links

ENSG00000141580 ∙ NCBI:56270 ∙ OMIM:609226 ∙ HGNC:25072 ∙ Uniprot:Q5MNZ6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures	AR	General	Genetic knowledge may potentially be beneficial related to manifestations such as renal issues; Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	21937992; 28503735

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WDR45B gene.

• not provided (11 variants)
• Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures (7 variants)
• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR45B 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				6	1	7
missense			10	1		11
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		3	4
Total	0	1	11	7	4

Variants in WDR45B

This is a list of pathogenic ClinVar variants found in the WDR45B region.

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

Position	Type	Phenotype	Significance	ClinVar
17-82615954-C-T		Inborn genetic diseases	Uncertain significance (Apr 27, 2023)
17-82615986-T-C		Inborn genetic diseases	Uncertain significance (Nov 20, 2023)
17-82616012-G-A		Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures	Benign/Likely benign (Jan 01, 2024)
17-82616534-G-A			Likely benign (Jul 17, 2018)
17-82616656-A-G		Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures	Benign (Dec 05, 2021)
17-82617303-G-A		Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures	Pathogenic (Sep 20, 2021)
17-82617355-G-A			Benign (Oct 10, 2018)
17-82617363-C-T		Inborn genetic diseases	Uncertain significance (Nov 28, 2023)
17-82617395-A-G		Inborn genetic diseases	Uncertain significance (Feb 07, 2023)
17-82619070-C-G		Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures	Uncertain significance (-)
17-82619074-G-A		Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures	Likely pathogenic (-)
17-82619138-ACA-CCG			Uncertain significance (Feb 25, 2020)
17-82621693-G-A			Likely benign (Sep 01, 2021)
17-82621706-G-A		Inborn genetic diseases	Uncertain significance (Oct 12, 2022)
17-82627157-T-A		Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures	Benign (Dec 05, 2021)
17-82627213-C-T		Inborn genetic diseases	Uncertain significance (Sep 15, 2021)
17-82627238-T-C		Inborn genetic diseases	Uncertain significance (Mar 06, 2023)
17-82627255-A-G		Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures	Uncertain significance (Jan 29, 2020)
17-82630966-C-T		Inborn genetic diseases	Uncertain significance (Mar 29, 2022)
17-82643985-A-G		Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures	Uncertain significance (Jul 27, 2020)
17-82643990-C-T		Inborn genetic diseases	Uncertain significance (Mar 24, 2023)
17-82643991-G-A		Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures	Likely pathogenic (Apr 01, 2023)
17-82644013-C-T			Likely benign (Jan 01, 2023)
17-82644032-G-A			Benign (Dec 31, 2019)
17-82648296-G-A			Likely benign (May 09, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR45B	protein_coding	protein_coding	ENST00000392325	10	33992

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.156	0.843	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	150	189	0.793	0.0000112	2268
Missense in Polyphen		18	39.426	0.45655		471
Synonymous	-0.863	88	78.3	1.12	0.00000558	646
Loss of Function	2.99	5	19.1	0.262	0.00000110	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000324	0.000323
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Macroautophagy;Cellular responses to external stimuli (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.324
• hipred: Y
• hipred_score: 0.728
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr45b

Gene ontology

• Biological process: autophagosome assembly;autophagy of mitochondrion;protein lipidation;cellular response to starvation;protein localization to phagophore assembly site
• Cellular component: phagophore assembly site;lysosome;cytosol;extrinsic component of membrane;phagophore assembly site membrane
• Molecular function: protein binding;phosphatidylinositol-3-phosphate binding;TSC1-TSC2 complex binding;phosphatidylinositol-3,5-bisphosphate binding