FOXD4

forkhead box D4, the group of Forkhead boxes

Basic information

Region (hg38): 9:116231-118417

Previous symbols: [ "FKHL9" ]

Links

ENSG00000170122 ∙ NCBI:2298 ∙ OMIM:601092 ∙ HGNC:3805 ∙ Uniprot:Q12950 ∙ 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 FOXD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXD4 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						0
missense			56	4		60
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	57	4	0

Variants in FOXD4

This is a list of pathogenic ClinVar variants found in the FOXD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-116811-C-A		not specified	Uncertain significance (Jun 23, 2021)
9-116837-G-A		not specified	Uncertain significance (Jan 19, 2025)
9-116837-G-T		not specified	Uncertain significance (May 24, 2024)
9-116864-G-T		not specified	Uncertain significance (Jun 23, 2023)
9-116869-C-G		not specified	Uncertain significance (Jun 07, 2023)
9-116871-C-G		not specified	Uncertain significance (Apr 22, 2022)
9-116874-C-T		not specified	Likely benign (Jul 07, 2024)
9-116886-C-A		not specified	Uncertain significance (Jun 17, 2024)
9-116909-C-T		not specified	Uncertain significance (Jan 27, 2025)
9-116919-C-G		not specified	Uncertain significance (Apr 13, 2023)
9-116939-G-A		not specified	Uncertain significance (Feb 27, 2024)
9-116943-A-C			Uncertain significance (Feb 01, 2024)
9-116952-A-T		not specified	Uncertain significance (Oct 05, 2021)
9-116961-C-G		not specified	Likely benign (Sep 03, 2024)
9-116961-C-T		not specified	Likely benign (Feb 13, 2025)
9-116964-C-T		not specified	Uncertain significance (Sep 14, 2022)
9-116973-C-A		not specified	Uncertain significance (Feb 19, 2025)
9-116995-G-T		not specified	Uncertain significance (Mar 14, 2023)
9-117027-G-C		not specified	Uncertain significance (Jun 07, 2023)
9-117029-T-G		not specified	Uncertain significance (Jul 30, 2024)
9-117063-T-A		not specified	Uncertain significance (May 14, 2024)
9-117074-G-A		not specified	Uncertain significance (Nov 06, 2023)
9-117096-G-A		not specified	Uncertain significance (Jan 18, 2022)
9-117132-A-C		not specified	Uncertain significance (Jan 23, 2023)
9-117149-C-T		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXD4	protein_coding	protein_coding	ENST00000382500	1	2181

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000664	0.161	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-4.07	418	240	1.74	0.0000119	2710
Missense in Polyphen		119	62.826	1.8941		771
Synonymous	-4.84	171	107	1.59	0.00000546	972
Loss of Function	-0.626	7	5.43	1.29	2.45e-7	56

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

Intolerance Scores

• loftool: 0.239
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.14

Haploinsufficiency Scores

• pHI: 0.156

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0805

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxd4

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;anatomical structure morphogenesis;cell differentiation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;DNA binding, bending;sequence-specific DNA binding