FOXI1 forkhead box I1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: FOXI1provided by HGNC
Official Full Name: forkhead box I1provided by HGNC
Primary source: HGNC:HGNC:3815
See related: Ensembl:ENSG00000168269 MIM:601093; AllianceGenome:HGNC:3815
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HFH3; FKH10; HFH-3; FKHL10; FREAC6; FREAC-6
Summary: This gene belongs to the forkhead family of transcription factors, which is characterized by a distinct forkhead domain. This gene may play an important role in the development of the cochlea and vestibulum, as well as in embryogenesis. The encoded protein has been found to be required for the transcription of four subunits of a proton pump found in the inner ear, the kidney, and the epididymis. Mutations in this gene have been associated with deafness, autosomal recessive 4. [provided by RefSeq, Jan 2017]
Expression: Biased expression in kidney (RPKM 10.3), salivary gland (RPKM 2.7) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 5q35.1

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (170105897..170109737)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (170644375..170648215)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (169532901..169536741)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Homozygous Missense Variants in FOXI1 and TMPRSS3 Genes Associated with Non-syndromic Deafness in Moroccan Families.
Title: Homozygous Missense Variants in FOXI1 and TMPRSS3 Genes Associated with Non-syndromic Deafness in Moroccan Families.
[Analysis of genotypes on 850 newborns with SLC26A4 single-allele mutation and the phenotypes of those with second variant].
Title: [Analysis of genotypes on 850 newborns with SLC26A4 single-allele mutation and the phenotypes of those with second variant].
Analysis of SLC26A4, FOXI1, and KCNJ10 Gene Variants in Patients with Incomplete Partition of the Cochlea and Enlarged Vestibular Aqueduct (EVA) Anomalies.
Title: Analysis of SLC26A4, FOXI1, and KCNJ10 Gene Variants in Patients with Incomplete Partition of the Cochlea and Enlarged Vestibular Aqueduct (EVA) Anomalies.
[Diagnosis of a Chinese pedigree affected with autosomal recessive deafness 4 with enlarged vestibular aqueduct due to compound heterozygous variants of FOXI1 gene].
Title: [Diagnosis of a Chinese pedigree affected with autosomal recessive deafness 4 with enlarged vestibular aqueduct due to compound heterozygous variants of FOXI1 gene].
FOXI1 inhibits gastric cancer cell proliferation by activating miR-590/ATF3 axis via integrating ChIP-seq and RNA-seq data.
Title: FOXI1 inhibits gastric cancer cell proliferation by activating miR-590/ATF3 axis via integrating ChIP-seq and RNA-seq data.
FOXI1 expression in chromophobe renal cell carcinoma and renal oncocytoma: a study of The Cancer Genome Atlas transcriptome-based outlier mining and immunohistochemistry.
Title: FOXI1 expression in chromophobe renal cell carcinoma and renal oncocytoma: a study of The Cancer Genome Atlas transcriptome-based outlier mining and immunohistochemistry.
Next-generation sequencing-based mutation analysis of genes associated with enlarged vestibular aqueduct in Chinese families.
Title: Next-generation sequencing-based mutation analysis of genes associated with enlarged vestibular aqueduct in Chinese families.
These data suggest that individuals with an SLC26A4 single-allele mutation, combined with FOXI1 or KCNJ10 gene mutations, do not suffer hearing loss during infancy
Title: Analysis of mutations in the FOXI1 and KCNJ10 genes in infants with a single-allele SLC26A4 mutation.
A substantial proportion of patients with a clinical diagnosis of inherited distal renal tubular acidosis has no identified causative mutations in currently known disease genes. Our data suggest that recessive mutations in FOXI1 can explain the disease in a subset of these patients.
Title: Acidosis and Deafness in Patients with Recessive Mutations in FOXI1.
Study found positive nuclear FOXI1 staining in 96% of renal oncocytoma (RO) and only 3% of chromophobe renal cell carcinoma (chRCC) and none of other types of renal cell tumor, including 'oncocytic' cellular variants. These findings suggest that FOXI1 immunohistochemistry is useful in differential diagnosis of RO from chRCC with overlapping histology.
Title: FOXI1 Immunohistochemistry Differentiates Benign Renal Oncocytoma from Malignant Chromophobe Renal Cell Carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Autosomal recessive nonsyndromic hearing loss 4 MedGen: C3538946 OMIM: 600791 GeneReviews: Genetic Hearing Loss Overview, Pendred Syndrome / Nonsyndromic Enlarged Vestibular Aqueduct	Compare labs
Pendred syndrome MedGen: C0271829 OMIM: 274600 GeneReviews: Genetic Hearing Loss Overview, Pendred Syndrome / Nonsyndromic Enlarged Vestibular Aqueduct	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

bac51983S (e-PCR)
- UniSTS:181535

FOXI1_2406 (e-PCR)
- UniSTS:280676

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding, bending	NAS Non-traceable Author Statement more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in anatomical structure morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in embryo development ending in birth or egg hatching	NAS Non-traceable Author Statement more info	PubMed
involved_in inner ear morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleus	IC Inferred by Curator more info	PubMed

General protein information

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Preferred Names: forkhead box protein I1

Names: HNF-3/fork-head homolog-3; forkhead-like 10; forkhead-related activator 6; forkhead-related protein FKHL10; forkhead-related transcription factor 6; hepatocyte nuclear factor 3 forkhead homolog 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_012068.2 RefSeqGene

Range

4985..8822

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_012188.5 → NP_036320.2 forkhead box protein I1 isoform a

See identical proteins and their annotated locations for NP_036320.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AC008660, BC029778

Consensus CDS

CCDS4372.1

UniProtKB/Swiss-Prot

Q12951, Q14518, Q66SR7, Q8N6L8

UniProtKB/TrEMBL

A8K811, E0XEN6, E0XEY9

Related

ENSP00000304286.5, ENST00000306268.8

Conserved Domains (1) summary

smart00339
Location:123 → 211

FH; FORKHEAD
NM_144769.4 → NP_658982.1 forkhead box protein I1 isoform b

See identical proteins and their annotated locations for NP_658982.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame coding segment compared to variant 1, resulting in an isoform (b) that lacks an internal portion compared to isoform a.

Source sequence(s)

AC008660, BC029778

Consensus CDS

CCDS47337.1

UniProtKB/Swiss-Prot

Q12951

Related

ENSP00000415483.2, ENST00000449804.4

Conserved Domains (1) summary

pfam00250
Location:123 → 191

Forkhead; Forkhead domain