WDHD1

WD repeat and HMG-box DNA binding protein 1, the group of WD repeat domain containing

Basic information

Region (hg38): 14:54938949-55027105

Links

ENSG00000198554

∙ NCBI:11169 ∙ OMIM:608126 ∙ HGNC:23170 ∙ Uniprot:O75717 ∙ 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 WDHD1 gene.

not_specified (131 variants)
not_provided (14 variants)
WDHD1-related_disorder (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDHD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007086.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	4 clinvar	5
missense			123 clinvar	10 clinvar	4 clinvar	137
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	124	11	8

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDHD1	protein_coding	protein_coding	ENST00000360586	25	88156

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.37e-18	0.993	125490	0	258	125748	0.00103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.137	594	585	1.02	0.0000288	7448
Missense in Polyphen		142	162.95	0.87145		1966
Synonymous	0.903	180	196	0.918	0.00000979	2062
Loss of Function	2.85	38	62.2	0.610	0.00000339	744

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00163	0.00161
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000663	0.000598
Finnish	0.00248	0.00241
European (Non-Finnish)	0.000802	0.000774
Middle Eastern	0.000663	0.000598
South Asian	0.00210	0.00209
Other	0.000382	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication. {ECO:0000269|PubMed:19805216}.;
Pathway: Mesodermal Commitment Pathway (Consensus)

Recessive Scores

pRec: 0.0916

Intolerance Scores

loftool: 0.959
rvis_EVS: 0.79
rvis_percentile_EVS: 87.29

Haploinsufficiency Scores

pHI: 0.920
hipred: Y
hipred_score: 0.715
ghis: 0.591

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.789

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Wdhd1
Phenotype

Gene ontology

Biological process: mitotic cell cycle;DNA-dependent DNA replication;DNA repair;regulation of transcription by RNA polymerase II;cellular response to DNA damage stimulus
Cellular component: nucleoplasm;cytoplasm;replication fork protection complex;nuclear replication fork
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;chromatin binding;protein binding