FOXD1

forkhead box D1, the group of Forkhead boxes

Basic information

Region (hg38): 5:73444827-73448777

Previous symbols: [ "FKHL8" ]

Links

ENSG00000251493 ∙ NCBI:2297 ∙ OMIM:601091 ∙ HGNC:3802 ∙ Uniprot:Q16676 ∙ 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 FOXD1 gene.

• not_specified (44 variants)
• FOXD1-related_disorder (26 variants)
• Hereditary_breast_ovarian_cancer_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004472.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				22		22
missense			41	2		43
nonsense						0
start loss						0
frameshift				1		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	25	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXD1	protein_coding	protein_coding	ENST00000499003	1	3699

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.689	0.295	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.584	106	124	0.853	0.00000594	2805
Missense in Polyphen		20	47.332	0.42254		515
Synonymous	-0.418	62	58.0	1.07	0.00000281	1101
Loss of Function	1.81	0	3.82	0.00	1.63e-7	80

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	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor involved in regulation of gene expression in a variety of processes, including formation of positional identity in the developing retina, regionalization of the optic chiasm, morphogenesis of the kidney, and neuralization of ectodermal cells (By similarity). Involved in transcriptional activation of PGF and C3 genes (PubMed:27805902). {ECO:0000250|UniProtKB:Q61345, ECO:0000269|PubMed:27805902}.
• Pathway: Preimplantation Embryo (Consensus)

Haploinsufficiency Scores

• ghis: 0.468

Essentials

• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxd1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; renal/urinary system phenotype; vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;axon guidance;anatomical structure morphogenesis;positive regulation of gene expression;cell differentiation;positive regulation of BMP signaling pathway;luteinizing hormone secretion;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;dichotomous subdivision of terminal units involved in ureteric bud branching;nephrogenic mesenchyme development;metanephric nephron development;metanephric capsule development;metanephric capsule specification;positive regulation of kidney development
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;DNA binding, bending;sequence-specific DNA binding