FOXN4

forkhead box N4, the group of Forkhead boxes

Basic information

Region (hg38): 12:109277978-109309284

Links

ENSG00000139445

∙ NCBI:121643 ∙ OMIM:609429 ∙ HGNC:21399 ∙ Uniprot:Q96NZ1 ∙ 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 FOXN4 gene.

not_specified (71 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXN4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000213596.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			71 clinvar			71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	71	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXN4	protein_coding	protein_coding	ENST00000299162	9	31242

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.861	0.139	125681	0	9	125690	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	242	302	0.801	0.0000182	3312
Missense in Polyphen		82	100.66	0.81461		1053
Synonymous	1.05	120	136	0.885	0.00000945	1082
Loss of Function	3.48	3	19.6	0.153	0.00000106	220

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000155	0.000153
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000358	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000657	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Transcription factor essential for neural and some non- neural tissues development, such as retina and lung respectively. Binds to an 11-bp consensus sequence containing the invariant tetranucleotide 5'-ACGC-3'. During development of the central nervous system, is required to specify the amacrine and horizontal cell fates from multipotent retinal progenitors while suppressing the alternative photoreceptor cell fates through activating DLL4- NOTCH signaling. Also acts synergistically with ASCL1/MASH1 to activate DLL4-NOTCH signaling and drive commitment of p2 progenitors to the V2b interneuron fates during spinal cord neurogenesis. In development of non-neural tissues, plays an essential role in the specification of the atrioventricular canal and is indirectly required for patterning the distal airway during lung development (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.152

Intolerance Scores

loftool: 0.255
rvis_EVS: -0.14
rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

pHI: 0.167
hipred: N
hipred_score: 0.411
ghis: 0.462

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.204

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Foxn4
Phenotype: cellular phenotype; 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); vision/eye 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);

Zebrafish Information Network

Gene name: foxn4
Affected structure: heart valve
Phenotype tag: abnormal
Phenotype quality: morphology

Gene ontology

Biological process: heart looping;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;regulation of heart contraction;retina layer formation;amacrine cell differentiation;atrioventricular canal development;positive regulation of transcription, DNA-templated;ventral spinal cord interneuron fate commitment
Cellular component: nucleus
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;enhancer sequence-specific DNA binding;chromatin binding;DNA-binding transcription factor activity;protein binding