FOXI2

forkhead box I2, the group of Forkhead boxes

Basic information

Region (hg38): 10:127737185-127741183

Links

ENSG00000186766 ∙ NCBI:399823 ∙ OMIM:617202 ∙ HGNC:32448 ∙ Uniprot:Q6ZQN5 ∙ 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 FOXI2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXI2 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	1
missense			42	1		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	1	1

Variants in FOXI2

This is a list of pathogenic ClinVar variants found in the FOXI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-127737277-G-A		not specified	Uncertain significance (Apr 01, 2024)
10-127737326-C-T		not specified	Uncertain significance (Apr 25, 2023)
10-127737344-C-T		not specified	Uncertain significance (Jan 03, 2025)
10-127737347-C-T		not specified	Uncertain significance (Feb 21, 2024)
10-127737362-G-A		not specified	Uncertain significance (Sep 02, 2024)
10-127737372-C-A			Benign (May 18, 2018)
10-127737385-G-A		not specified	Uncertain significance (Sep 12, 2023)
10-127737388-C-T		not specified	Uncertain significance (Aug 20, 2024)
10-127737405-C-G		not specified	Uncertain significance (Jul 11, 2023)
10-127737430-T-C		not specified	Uncertain significance (Dec 14, 2023)
10-127737455-C-A		not specified	Uncertain significance (Aug 23, 2021)
10-127737470-C-G		not specified	Uncertain significance (Jun 25, 2024)
10-127737476-A-G		not specified	Uncertain significance (Oct 20, 2024)
10-127737506-C-T		not specified	Uncertain significance (Aug 12, 2021)
10-127737509-G-A		not specified	Uncertain significance (Sep 26, 2024)
10-127737527-A-C		not specified	Uncertain significance (Sep 17, 2021)
10-127737533-C-A		not specified	Uncertain significance (Sep 02, 2024)
10-127737535-T-C		not specified	Uncertain significance (Sep 30, 2024)
10-127737566-T-C		not specified	Uncertain significance (Nov 17, 2023)
10-127737590-C-G		not specified	Uncertain significance (Aug 21, 2024)
10-127737610-A-G		not specified	Uncertain significance (Jun 02, 2024)
10-127737628-C-G		not specified	Uncertain significance (Feb 17, 2022)
10-127737663-G-C		not specified	Uncertain significance (Nov 24, 2024)
10-127737668-T-A		not specified	Uncertain significance (May 02, 2024)
10-127737707-G-A		not specified	Uncertain significance (Feb 06, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXI2	protein_coding	protein_coding	ENST00000388920	2	3952

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000299	0.364	124960	0	23	124983	0.0000920

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0918	139	136	1.02	0.00000649	1971
Missense in Polyphen		40	53.388	0.74924		680
Synonymous	-0.879	69	60.3	1.14	0.00000315	699
Loss of Function	-0.174	5	4.60	1.09	1.98e-7	66

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)	0.0000573	0.0000530
Middle Eastern	0.00	0.00
South Asian	0.000568	0.000557
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible transcriptional activator. {ECO:0000250}.

Haploinsufficiency Scores

• pHI: 0.0596
• hipred: N
• hipred_score: 0.453

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.217

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxi2
• Phenotype: normal 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;anatomical structure morphogenesis;cell differentiation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding