FOXK2

forkhead box K2, the group of Forkhead boxes

Basic information

Region (hg38): 17:82519712-82644662

Previous symbols: [ "ILF", "ILF1" ]

Links

ENSG00000141568 ∙ NCBI:3607 ∙ OMIM:147685 ∙ HGNC:6036 ∙ Uniprot:Q01167 ∙ 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 FOXK2 gene.

• Inborn genetic diseases (42 variants)
• not provided (29 variants)
• Premature ovarian insufficiency (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXK2 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				6	8	14
missense			41	3	3	47
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)				1	1	2
splice region				1	1	2
non coding				3	2	5
Total	0	0	41	14	14

Variants in FOXK2

This is a list of pathogenic ClinVar variants found in the FOXK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-82519895-G-T		not specified	Uncertain significance (Apr 13, 2022)
17-82519901-G-C		not specified	Uncertain significance (Aug 16, 2022)
17-82519932-C-T		not specified	Uncertain significance (Sep 06, 2022)
17-82519935-CGGGCGGCGGGGCCGG-C			Likely benign (Dec 31, 2019)
17-82519941-G-T		not specified	Uncertain significance (Sep 14, 2022)
17-82519947-C-T		not specified	Uncertain significance (Sep 06, 2022)
17-82519953-G-A		not specified	Uncertain significance (Aug 28, 2023)
17-82519963-C-A			Likely benign (Jan 08, 2019)
17-82520042-C-T		Premature ovarian insufficiency	Likely benign (Jul 21, 2018)
17-82520116-C-T			Benign (Jun 18, 2018)
17-82520186-C-T		not specified	Uncertain significance (May 17, 2023)
17-82520211-G-A		not specified	Uncertain significance (Feb 22, 2023)
17-82520283-C-T		not specified	Uncertain significance (May 16, 2023)
17-82520306-G-A		not specified	Uncertain significance (Jan 31, 2024)
17-82520314-G-T			Likely benign (Jul 25, 2017)
17-82563382-A-G		not specified	Uncertain significance (Sep 27, 2021)
17-82563392-C-T		not specified	Uncertain significance (Jul 11, 2022)
17-82563427-C-G		not specified	Uncertain significance (Jan 04, 2022)
17-82563473-C-T		not specified	Uncertain significance (Sep 22, 2023)
17-82568137-A-G		not specified	Likely benign (Jan 03, 2024)
17-82571738-G-T			Benign (Dec 31, 2019)
17-82571776-C-T		not specified	Uncertain significance (Jan 17, 2023)
17-82571807-C-T			Benign (Aug 15, 2018)
17-82571836-A-T		not specified	Uncertain significance (May 17, 2023)
17-82571860-A-G		not specified	Uncertain significance (Jan 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXK2	protein_coding	protein_coding	ENST00000335255	9	124950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0255	0.974	125515	9	215	125739	0.000891

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.396	364	386	0.943	0.0000240	4173
Missense in Polyphen		67	118.82	0.56387		1378
Synonymous	-2.65	227	182	1.25	0.0000132	1464
Loss of Function	3.05	7	22.7	0.309	0.00000115	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00216	0.00184
Ashkenazi Jewish	0.000203	0.000198
East Asian	0.00452	0.00414
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000267	0.000255
Middle Eastern	0.00452	0.00414
South Asian	0.00269	0.00255
Other	0.000663	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional regulator that recognizes the core sequence 5'-TAAACA-3'. Binds to NFAT-like motifs (purine-rich) in the IL2 promoter (PubMed:1339390). Positively regulates WNT/beta- catenin signaling by translocating DVL proteins into the nucleus (PubMed:25805136). Also binds to HIV-1 long terminal repeat. May be involved in both positive and negative regulation of important viral and cellular promoter elements (PubMed:1909027). {ECO:0000269|PubMed:1339390, ECO:0000269|PubMed:1909027, ECO:0000269|PubMed:25805136}.
• Pathway: Post-translational protein modification;Metabolism of proteins;UCH proteinases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.204

Intolerance Scores

• loftool: 0.0444
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.84

Haploinsufficiency Scores

• pHI: 0.522
• hipred: Y
• hipred_score: 0.685
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.938

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxk2

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;protein deubiquitination;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm
• Molecular function: magnesium ion binding;transcription regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding