FOXD4L3

forkhead box D4 like 3, the group of Forkhead boxes

Basic information

Region (hg38): 9:68302867-68305084

Links

ENSG00000187559 ∙ NCBI:286380 ∙ OMIM:611086 ∙ HGNC:18523 ∙ Uniprot:Q6VB84 ∙ 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 FOXD4L3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXD4L3 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				3		3
missense			51	6		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	51	9	0

Variants in FOXD4L3

This is a list of pathogenic ClinVar variants found in the FOXD4L3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-68302967-G-A		not specified	Likely benign (Oct 12, 2021)
9-68303024-G-A		not specified	Uncertain significance (Jan 22, 2025)
9-68303024-G-C		not specified	Uncertain significance (Feb 17, 2022)
9-68303061-A-G		not specified	Uncertain significance (Nov 08, 2024)
9-68303073-A-C		not specified	Uncertain significance (Sep 20, 2024)
9-68303084-G-A		not specified	Uncertain significance (May 14, 2024)
9-68303085-C-T		not specified	Uncertain significance (Jul 06, 2021)
9-68303089-G-A			Likely benign (Mar 01, 2023)
9-68303092-C-A		not specified	Uncertain significance (Jan 19, 2025)
9-68303114-C-T		not specified	Uncertain significance (Jan 02, 2024)
9-68303171-A-G		not specified	Uncertain significance (Jan 30, 2024)
9-68303175-A-T		not specified	Uncertain significance (Feb 03, 2025)
9-68303180-G-A		not specified	Uncertain significance (Dec 26, 2024)
9-68303222-A-T		not specified	Uncertain significance (Dec 03, 2021)
9-68303238-C-T		not specified	Uncertain significance (Jun 07, 2024)
9-68303241-C-T		not specified	Uncertain significance (May 15, 2023)
9-68303262-G-A		not specified	Uncertain significance (Jul 26, 2021)
9-68303280-C-G		not specified	Uncertain significance (Feb 17, 2022)
9-68303388-G-A		not specified	Uncertain significance (Dec 13, 2024)
9-68303402-G-A		not specified	Uncertain significance (Mar 14, 2023)
9-68303409-A-G		not specified	Uncertain significance (Jan 23, 2023)
9-68303417-A-C		not specified	Uncertain significance (Nov 27, 2023)
9-68303501-C-G		not specified	Uncertain significance (Jun 24, 2022)
9-68303502-T-C		not specified	Uncertain significance (Oct 16, 2024)
9-68303505-A-C		not specified	Uncertain significance (Feb 12, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXD4L3	protein_coding	protein_coding	ENST00000342833	1	2725

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.495	0.436	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.68	95	58.7	1.62	0.00000290	2545
Missense in Polyphen		11	5.5048	1.9983		728
Synonymous	-1.34	36	27.1	1.33	0.00000143	883
Loss of Function	1.28	0	1.90	0.00	8.36e-8	97

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

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.108

Gene Damage Prediction

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