WDR49

WD repeat domain 49, the group of WD repeat domain containing

Basic information

Region (hg38): 3:167478683-167653983

Links

ENSG00000174776 ∙ NCBI:151790 ∙ ∙ HGNC:26587 ∙ Uniprot:Q8IV35 ∙ 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 WDR49 gene.

• Inborn genetic diseases (39 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR49 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				1		1
missense			35	4		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	5	0

Variants in WDR49

This is a list of pathogenic ClinVar variants found in the WDR49 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-167478907-T-A		not specified	Uncertain significance (Mar 02, 2023)
3-167478956-C-G		not specified	Uncertain significance (Mar 24, 2023)
3-167478984-A-G		not specified	Uncertain significance (Dec 27, 2023)
3-167500155-T-C		not specified	Uncertain significance (Sep 14, 2022)
3-167500167-G-A		not specified	Uncertain significance (Jun 29, 2023)
3-167500177-G-T		not specified	Uncertain significance (May 06, 2022)
3-167500192-C-G		not specified	Uncertain significance (Nov 14, 2023)
3-167500192-C-T		not specified	Uncertain significance (Nov 18, 2022)
3-167500290-C-G		not specified	Uncertain significance (Jun 24, 2022)
3-167505320-T-C		not specified	Uncertain significance (Oct 06, 2022)
3-167505365-A-T		not specified	Uncertain significance (Sep 16, 2021)
3-167505396-A-G		not specified	Uncertain significance (Dec 14, 2023)
3-167522336-T-C		not specified	Uncertain significance (Aug 08, 2022)
3-167522363-G-C		not specified	Uncertain significance (Oct 27, 2022)
3-167522427-C-T		not specified	Likely benign (Sep 28, 2022)
3-167527867-T-C		not specified	Likely benign (Jul 09, 2021)
3-167527873-A-G		not specified	Uncertain significance (Jan 23, 2023)
3-167527936-T-C		not specified	Uncertain significance (Dec 20, 2023)
3-167527938-C-T		not specified	Likely benign (Jan 31, 2024)
3-167527959-G-T		Malignant tumor of prostate	Uncertain significance (-)
3-167527977-G-A		not specified	Uncertain significance (Oct 05, 2021)
3-167528011-A-T		not specified	Uncertain significance (Nov 13, 2023)
3-167528015-C-A		not specified	Uncertain significance (Apr 25, 2022)
3-167529119-G-C		not specified	Uncertain significance (Aug 19, 2021)
3-167529179-T-C		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR49	protein_coding	protein_coding	ENST00000308378	14	175300

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.05e-19	0.00864	125574	0	174	125748	0.000692

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.439	372	349	1.07	0.0000166	4617
Missense in Polyphen		90	69.971	1.2863		945
Synonymous	1.35	103	122	0.844	0.00000598	1251
Loss of Function	0.490	31	34.1	0.909	0.00000173	437

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00206	0.00206
Ashkenazi Jewish	0.00	0.00
East Asian	0.00300	0.00299
Finnish	0.00	0.00
European (Non-Finnish)	0.000427	0.000413
Middle Eastern	0.00300	0.00299
South Asian	0.000409	0.000392
Other	0.00156	0.00147

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.974
• rvis_EVS: 0.34
• rvis_percentile_EVS: 73.68

Haploinsufficiency Scores

• pHI: 0.0868
• hipred: N
• hipred_score: 0.144
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.127

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr49