WDR72

WD repeat domain 72, the group of WD repeat domain containing

Basic information

Region (hg38): 15:53513740-53762878

Links

ENSG00000166415 ∙ NCBI:256764 ∙ OMIM:613214 ∙ HGNC:26790 ∙ Uniprot:Q3MJ13 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• amelogenesis imperfecta type 2 (Supportive), mode of inheritance: AR
• amelogenesis imperfecta hypomaturation type 2A3 (Moderate), mode of inheritance: AR
• renal tubular acidosis (Limited), mode of inheritance: AR
• amelogenesis imperfecta hypomaturation type 2A3 (Strong), mode of inheritance: AR
• amelogenesis imperfecta (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Amelogenesis imperfecta, hypomaturation type, IIA3	AR	General	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	Dental	19853237; 22243262; 23293580

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WDR72 gene.

• Amelogenesis imperfecta hypomaturation type 2A3 (148 variants)
• Amelogenesis Imperfecta, Recessive (75 variants)
• Inborn genetic diseases (51 variants)
• not provided (35 variants)
• not specified (6 variants)
• Renal tubular acidosis, distal, 4, with hemolytic anemia;Amelogenesis imperfecta hypomaturation type 2A3 (1 variants)
• Renal tubular acidosis, distal, 4, with hemolytic anemia (1 variants)
• Amelogenesis imperfecta (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR72 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			11	3	1	15
missense		1	69	8	2	80
nonsense	3	3				6
start loss						0
frameshift	1	2				3
inframe indel						0
splice donor/acceptor (+/-2bp)		1	1			2
splice region			6	2		8
non coding			107	28	36	171
Total	4	7	188	39	39

Highest pathogenic variant AF is 0.0000329

Variants in WDR72

This is a list of pathogenic ClinVar variants found in the WDR72 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-53513763-C-T		Amelogenesis Imperfecta, Recessive	Likely benign (Jun 14, 2016)
15-53513847-A-C		Amelogenesis imperfecta hypomaturation type 2A3	Uncertain significance (Jan 13, 2018)
15-53513889-A-T		Amelogenesis imperfecta hypomaturation type 2A3	Uncertain significance (Jan 12, 2018)
15-53513957-C-G		Amelogenesis Imperfecta, Recessive	Likely benign (Jun 14, 2016)
15-53513965-T-C		Amelogenesis imperfecta hypomaturation type 2A3	Likely benign (Jan 13, 2018)
15-53514008-C-A		Amelogenesis imperfecta hypomaturation type 2A3	Uncertain significance (Jan 13, 2018)
15-53514010-T-C		Amelogenesis imperfecta hypomaturation type 2A3	Likely benign (Jan 13, 2018)
15-53514049-T-C		Amelogenesis imperfecta hypomaturation type 2A3	Uncertain significance (Jan 12, 2018)
15-53514072-G-A		Amelogenesis imperfecta hypomaturation type 2A3	Uncertain significance (Jan 12, 2018)
15-53514105-T-G		Amelogenesis imperfecta hypomaturation type 2A3	Uncertain significance (Jan 13, 2018)
15-53514107-T-C		Amelogenesis imperfecta hypomaturation type 2A3	Likely benign (Jan 13, 2018)
15-53514124-A-G		Amelogenesis imperfecta hypomaturation type 2A3	Likely benign (Jan 12, 2018)
15-53514185-C-A		Amelogenesis imperfecta hypomaturation type 2A3	Uncertain significance (Jan 12, 2018)
15-53514188-T-C		Amelogenesis imperfecta hypomaturation type 2A3	Uncertain significance (Jan 13, 2018)
15-53514229-G-A		Amelogenesis imperfecta hypomaturation type 2A3	Uncertain significance (Jan 13, 2018)
15-53514240-G-A		Amelogenesis imperfecta hypomaturation type 2A3	Uncertain significance (Jan 13, 2018)
15-53514266-C-T		Amelogenesis imperfecta hypomaturation type 2A3	Likely benign (Jan 12, 2018)
15-53514276-T-G		Amelogenesis imperfecta hypomaturation type 2A3	Benign (Jan 13, 2018)
15-53514365-T-C		Amelogenesis imperfecta hypomaturation type 2A3	Uncertain significance (Jan 13, 2018)
15-53514374-C-T		Amelogenesis imperfecta hypomaturation type 2A3	Likely benign (Jan 12, 2018)
15-53514474-A-C		Amelogenesis imperfecta hypomaturation type 2A3	Benign (Apr 27, 2017)
15-53514535-A-G		Amelogenesis Imperfecta, Recessive	Likely benign (Jun 14, 2016)
15-53514571-C-T		Amelogenesis imperfecta hypomaturation type 2A3	Uncertain significance (Jan 12, 2018)
15-53514573-A-G		Amelogenesis imperfecta hypomaturation type 2A3	Uncertain significance (Jan 12, 2018)
15-53514585-T-C		Amelogenesis Imperfecta, Recessive	Likely benign (Jun 14, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR72	protein_coding	protein_coding	ENST00000396328	19	249138

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.73e-27	0.00550	125562	0	186	125748	0.000740

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.956	617	554	1.11	0.0000259	7231
Missense in Polyphen		166	165.41	1.0036		2255
Synonymous	-0.485	206	197	1.04	0.00000968	2075
Loss of Function	1.10	46	54.8	0.840	0.00000274	699

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00132	0.00131
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000927	0.000925
Finnish	0.000604	0.000601
European (Non-Finnish)	0.000858	0.000853
Middle Eastern	0.000927	0.000925
South Asian	0.000686	0.000686
Other	0.000493	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a major role in formation of tooth enamel (PubMed:19853237, PubMed:25008349). Specifically required during the maturation phase of amelogenesis for normal formation of the enamel matrix and clearance of enamel proteins. May be involved in localization of the calcium transporter SLC24A4 to the ameloblast cell membrane. {ECO:0000250|UniProtKB:D3YYM4, ECO:0000269|PubMed:19853237, ECO:0000269|PubMed:25008349}.
• Disease: DISEASE: Amelogenesis imperfecta, hypomaturation type, 2A3 (AI2A3) [MIM:613211]: A defect of enamel formation. The disorder involves both primary and secondary dentitions. The teeth have a shiny agar jelly appearance and the enamel is softer than normal. Brown pigment is present in middle layers of enamel. {ECO:0000269|PubMed:19853237, ECO:0000269|PubMed:25008349}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.0874

Intolerance Scores

• loftool: 0.979
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.35

Haploinsufficiency Scores

• pHI: 0.0498
• hipred: N
• hipred_score: 0.169
• ghis: 0.476

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	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Wdr72
• Phenotype: skeleton phenotype; craniofacial phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: enamel mineralization
• Cellular component: cytoplasm;endosome