FOXD2

forkhead box D2, the group of Forkhead boxes

Basic information

Region (hg38): 1:47438044-47440691

Previous symbols: [ "FKHL17" ]

Links

ENSG00000186564 ∙ NCBI:2306 ∙ OMIM:602211 ∙ HGNC:3803 ∙ Uniprot:O60548 ∙ 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 FOXD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXD2 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		1
missense			45	2	1	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	3	1

Variants in FOXD2

This is a list of pathogenic ClinVar variants found in the FOXD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-47438148-A-G		not specified	Uncertain significance (Dec 30, 2024)
1-47438173-C-G		not specified	Uncertain significance (Aug 03, 2022)
1-47438215-T-C		not specified	Uncertain significance (Dec 11, 2024)
1-47438232-G-T		not specified	Uncertain significance (Sep 20, 2024)
1-47438241-G-A		not specified	Uncertain significance (Apr 12, 2023)
1-47438259-C-T		not specified	Uncertain significance (Sep 22, 2023)
1-47438260-G-A		not specified	Uncertain significance (Jan 24, 2024)
1-47438271-C-T		not specified	Uncertain significance (Nov 21, 2024)
1-47438280-C-T		not specified	Uncertain significance (Oct 20, 2024)
1-47438286-G-A		not specified	Uncertain significance (Mar 26, 2024)
1-47438292-C-T		not specified	Uncertain significance (Feb 14, 2025)
1-47438295-C-G		not specified	Uncertain significance (Dec 21, 2022)
1-47438323-C-A		not specified	Uncertain significance (Jul 08, 2022)
1-47438328-G-A			Benign (Jun 18, 2018)
1-47438333-C-G		not specified	Uncertain significance (Nov 14, 2023)
1-47438362-G-T		not specified	Uncertain significance (Jul 13, 2021)
1-47438374-G-A		not specified	Uncertain significance (Feb 28, 2023)
1-47438374-G-T		not specified	Uncertain significance (Nov 12, 2021)
1-47438397-C-G		not specified	Uncertain significance (Feb 02, 2024)
1-47438403-G-A		not specified	Uncertain significance (Dec 27, 2022)
1-47438412-G-A		not specified	Uncertain significance (May 13, 2024)
1-47438424-C-A		not specified	Uncertain significance (Jan 22, 2025)
1-47438442-G-T		not specified	Uncertain significance (Jun 06, 2023)
1-47438443-C-G		not specified	Uncertain significance (Dec 17, 2024)
1-47438495-G-A			Likely benign (Jun 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXD2	protein_coding	protein_coding	ENST00000334793	1	4675

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0290	0.816	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	148	186	0.794	0.00000882	3008
Missense in Polyphen		16	46.455	0.34442		516
Synonymous	-1.18	103	88.9	1.16	0.00000441	1146
Loss of Function	1.09	3	5.86	0.512	2.53e-7	91

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: Probable transcription factor involved in embryogenesis and somatogenesis. {ECO:0000250}.

Haploinsufficiency Scores

• pHI: 0.494
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.193

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxd2
• Phenotype: renal/urinary system phenotype

Gene ontology

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