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.

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.

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				4		4
missense			26	1		27
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	6	0

Variants in FOXD1

This is a list of pathogenic ClinVar variants found in the FOXD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-73447067-G-GGCGGCC		FOXD1-related disorder	Likely benign (Jun 03, 2019)
5-73447103-G-A		FOXD1-related disorder	Likely benign (Apr 27, 2021)
5-73447112-G-T		FOXD1-related disorder	Likely benign (Apr 08, 2022)
5-73447175-C-CGGCGAG		FOXD1-related disorder	Likely benign (May 20, 2022)
5-73447202-GGCGGCGGCGGCCTGC-G		FOXD1-related disorder	Benign (May 14, 2019)
5-73447220-G-A		not specified	Likely benign (Aug 18, 2017)
5-73447358-G-A		FOXD1-related disorder • not specified	Likely benign (Jul 19, 2023)
5-73447472-G-GGC		FOXD1-related disorder	Likely benign (Jan 28, 2021)
5-73447505-C-T		FOXD1-related disorder	Likely benign (Oct 13, 2021)
5-73447565-C-T		FOXD1-related disorder	Likely benign (Jul 12, 2022)
5-73447574-C-G		FOXD1-related disorder	Likely benign (Dec 12, 2022)
5-73447604-G-C		FOXD1-related disorder	Likely benign (Aug 30, 2021)
5-73447607-T-C		FOXD1-related disorder	Likely benign (Aug 30, 2021)
5-73447619-C-A		FOXD1-related disorder	Likely benign (Dec 05, 2022)
5-73447660-C-T		not specified	Uncertain significance (Jul 05, 2024)
5-73447682-G-T		FOXD1-related disorder	Likely benign (Sep 25, 2019)
5-73447696-G-A		not specified	Uncertain significance (Dec 22, 2023)
5-73447735-C-G		not specified	Uncertain significance (Jan 24, 2025)
5-73447751-C-T		FOXD1-related disorder	Likely benign (Sep 25, 2019)
5-73447754-C-G		FOXD1-related disorder	Likely benign (Mar 02, 2021)
5-73447798-C-T		not specified	Uncertain significance (Dec 06, 2023)
5-73447799-G-C		FOXD1-related disorder	Likely benign (Mar 02, 2021)
5-73447877-G-A		FOXD1-related disorder	Likely benign (Mar 16, 2020)
5-73447948-G-C		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)
5-73447983-G-C		not specified	Uncertain significance (Jun 17, 2024)

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