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.

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.

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	4	5
missense			52	5	5	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			1		1	2
non coding						0
Total	0	0	53	6	9

Variants in WDHD1

This is a list of pathogenic ClinVar variants found in the WDHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-54941572-T-C		not specified	Uncertain significance (Jun 10, 2022)
14-54941585-T-C		not specified	Uncertain significance (Dec 13, 2023)
14-54941632-C-G		not specified	Uncertain significance (Apr 18, 2024)
14-54941681-T-G			Benign (Apr 04, 2018)
14-54941691-C-T			Uncertain significance (Mar 01, 2019)
14-54944434-A-G			Benign (Jan 30, 2018)
14-54955598-G-C		not specified	Uncertain significance (Mar 20, 2024)
14-54955599-G-A			Benign (Dec 31, 2019)
14-54955676-A-T		not specified	Uncertain significance (Jan 26, 2022)
14-54957044-T-A		not specified	Uncertain significance (Dec 28, 2023)
14-54957113-G-T		not specified	Uncertain significance (Dec 15, 2022)
14-54957123-A-G		not specified	Uncertain significance (Dec 18, 2023)
14-54957608-C-T		not specified	Uncertain significance (Feb 05, 2024)
14-54962534-T-C		not specified	Uncertain significance (Sep 22, 2022)
14-54962541-C-T			Benign (Jul 04, 2018)
14-54962779-C-T		not specified	Uncertain significance (May 11, 2022)
14-54962832-C-A		not specified	Uncertain significance (Apr 06, 2023)
14-54962848-C-T		not specified	Uncertain significance (Jan 10, 2022)
14-54962857-A-G			Benign (Feb 26, 2018)
14-54962958-T-C		not specified	Uncertain significance (Oct 06, 2021)
14-54963001-C-G		not specified	Uncertain significance (Feb 23, 2023)
14-54963007-T-C		not specified	Uncertain significance (Mar 31, 2023)
14-54963063-A-G		not specified	Uncertain significance (Sep 26, 2022)
14-54963078-C-T		not specified	Uncertain significance (Jan 02, 2024)
14-54963079-G-A		not specified	Uncertain significance (Feb 26, 2024)

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

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