FOXD4L1

forkhead box D4 like 1, the group of Forkhead boxes

Basic information

Region (hg38): 2:113498665-113501150

Links

ENSG00000184492 ∙ NCBI:200350 ∙ OMIM:611084 ∙ HGNC:18521 ∙ Uniprot:Q9NU39 ∙ 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 FOXD4L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXD4L1 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				2		2
missense			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	3	0

Variants in FOXD4L1

This is a list of pathogenic ClinVar variants found in the FOXD4L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-113499278-C-A		not specified	Uncertain significance (Feb 16, 2023)
2-113499293-C-G		not specified	Uncertain significance (Jan 28, 2025)
2-113499336-T-C		not specified	Uncertain significance (Jun 09, 2022)
2-113499344-C-G		not specified	Uncertain significance (Jan 16, 2024)
2-113499356-G-A		not specified	Uncertain significance (Dec 19, 2023)
2-113499365-G-C		not specified	Uncertain significance (Jan 04, 2024)
2-113499383-G-A		not specified	Uncertain significance (Jan 04, 2022)
2-113499425-C-G		not specified	Uncertain significance (Sep 20, 2023)
2-113499477-T-A		not specified	Uncertain significance (Apr 04, 2024)
2-113499486-G-A		not specified	Uncertain significance (Mar 01, 2023)
2-113499513-G-A		not specified	Uncertain significance (Oct 01, 2024)
2-113499538-G-T		not specified	Uncertain significance (Oct 10, 2023)
2-113499549-C-T		not specified	Uncertain significance (May 06, 2022)
2-113499573-C-A		not specified	Uncertain significance (May 04, 2023)
2-113499595-C-G		not specified	Uncertain significance (Sep 17, 2021)
2-113499677-T-C		not specified	Uncertain significance (Feb 17, 2024)
2-113499686-T-C		not specified	Uncertain significance (May 23, 2023)
2-113499704-G-A		not specified	Uncertain significance (Feb 07, 2025)
2-113499719-A-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
2-113499755-A-C		not specified	Uncertain significance (Mar 21, 2023)
2-113499760-C-G		not specified	Uncertain significance (Nov 10, 2022)
2-113499780-C-G		not specified	Uncertain significance (Feb 25, 2025)
2-113499783-G-C		not specified	Uncertain significance (Nov 25, 2024)
2-113499792-C-A			Likely benign (-)
2-113499859-G-C		not specified	Uncertain significance (Aug 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXD4L1	protein_coding	protein_coding	ENST00000306507	1	2068

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00766	0.794	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.316	251	237	1.06	0.0000111	2537
Missense in Polyphen		63	64.011	0.9842		718
Synonymous	0.150	105	107	0.982	0.00000520	928
Loss of Function	0.990	4	6.78	0.590	3.00e-7	71

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

Recessive Scores

• pRec: 0.0795

Intolerance Scores

• loftool: 0.217
• rvis_EVS: 1.62
• rvis_percentile_EVS: 95.96

Haploinsufficiency Scores

• pHI: 0.0580

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0160

Gene Damage Prediction

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

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;sequence-specific DNA binding