FOXP4

forkhead box P4, the group of MicroRNA protein coding host genes|Forkhead boxes

Basic information

Region (hg38): 6:41546381-41602384

Links

ENSG00000137166 ∙ NCBI:116113 ∙ OMIM:608924 ∙ HGNC:20842 ∙ Uniprot:Q8IVH2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FOXP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXP4 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	4	5
missense		1	42	1	2	46
nonsense			2			2
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5			5
Total	0	1	51	2	6

Variants in FOXP4

This is a list of pathogenic ClinVar variants found in the FOXP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-41546996-G-C		Lung adenocarcinoma	Uncertain significance (Jun 06, 2022)
6-41547096-T-C		Lung adenocarcinoma	Uncertain significance (Jun 06, 2022)
6-41565584-C-A		Lung adenocarcinoma	Uncertain significance (Jun 06, 2022)
6-41565770-G-T			Likely pathogenic (Dec 03, 2023)
6-41565807-G-A		not specified	Uncertain significance (Aug 23, 2021)
6-41565818-G-A		not specified	Uncertain significance (Jun 06, 2023)
6-41565835-G-A			Benign (Jun 22, 2021)
6-41565841-C-A			Benign (Jun 22, 2021)
6-41565857-G-A			Likely benign (Feb 01, 2024)
6-41565864-C-T		not specified	Uncertain significance (Aug 30, 2021)
6-41565885-C-T		not specified	Uncertain significance (Jun 07, 2023)
6-41565890-A-G		not specified	Uncertain significance (Nov 25, 2024)
6-41565894-A-G		not specified	Uncertain significance (Dec 19, 2022)
6-41565951-TC-T			Uncertain significance (Aug 24, 2018)
6-41565953-C-T		FOXP4-related disorder	Uncertain significance (Jun 19, 2023)
6-41578002-G-A		not specified	Uncertain significance (Oct 02, 2023)
6-41578050-A-G		not specified	Uncertain significance (Oct 07, 2024)
6-41578070-T-C		not specified	Uncertain significance (Jun 16, 2024)
6-41584841-C-T			Uncertain significance (Jul 15, 2024)
6-41584882-G-GC		Neurodevelopmental disorder	Uncertain significance (Oct 08, 2024)
6-41585463-G-A			Benign/Likely benign (Feb 01, 2023)
6-41585475-G-T		not specified	Uncertain significance (Jun 11, 2021)
6-41586795-T-C		Lung adenocarcinoma	Uncertain significance (Jun 06, 2022)
6-41586868-G-T		Lung adenocarcinoma	Uncertain significance (Jun 06, 2022)
6-41587084-A-C			Uncertain significance (Jan 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXP4	protein_coding	protein_coding	ENST00000373060	16	55959

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.982	0.0176	125737	0	8	125745	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	304	416	0.731	0.0000258	4361
Missense in Polyphen		95	163.72	0.58027		1737
Synonymous	-0.651	197	186	1.06	0.0000131	1363
Loss of Function	4.64	5	34.4	0.146	0.00000147	367

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor that represses lung-specific expression. {ECO:0000250}.

Recessive Scores

• pRec: 0.153

Intolerance Scores

• loftool: 0.0749
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.27

Haploinsufficiency Scores

• pHI: 0.553
• hipred: Y
• hipred_score: 0.735
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxp4
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); embryo phenotype; respiratory system 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding;metal ion binding