FOXQ1

forkhead box Q1, the group of Forkhead boxes

Basic information

Region (hg38): 6:1312098-1314758

Links

ENSG00000164379 ∙ NCBI:94234 ∙ OMIM:612788 ∙ HGNC:20951 ∙ Uniprot:Q9C009 ∙ 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 FOXQ1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXQ1 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				2	1	3
missense			74	2	1	77
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	74	4	2

Variants in FOXQ1

This is a list of pathogenic ClinVar variants found in the FOXQ1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-1312709-A-G		not specified	Uncertain significance (Jan 18, 2025)
6-1312733-C-A		not specified	Uncertain significance (Jun 29, 2023)
6-1312735-G-C		not specified	Uncertain significance (Jun 17, 2024)
6-1312768-G-A		not specified	Uncertain significance (Oct 06, 2022)
6-1312772-C-T		not specified	Uncertain significance (May 15, 2024)
6-1312807-G-A		not specified	Uncertain significance (Sep 20, 2023)
6-1312818-C-G		not specified	Uncertain significance (May 23, 2024)
6-1312862-C-T		not specified	Uncertain significance (May 31, 2023)
6-1312880-A-G		not specified	Uncertain significance (Sep 12, 2024)
6-1312883-C-T		not specified	Uncertain significance (May 09, 2023)
6-1312885-C-G		not specified	Uncertain significance (Jul 06, 2022)
6-1312893-C-A		not specified	Uncertain significance (Dec 21, 2023)
6-1312918-C-G		not specified	Uncertain significance (May 02, 2024)
6-1312919-C-A		not specified	Uncertain significance (Feb 26, 2024)
6-1312925-C-T		not specified	Uncertain significance (May 04, 2022)
6-1312930-G-A		not specified	Uncertain significance (May 06, 2024)
6-1312994-G-C		not specified	Uncertain significance (Jul 08, 2022)
6-1312999-G-A		not specified	Uncertain significance (Dec 17, 2024)
6-1313006-G-A			Likely benign (Dec 01, 2022)
6-1313011-G-A		not specified	Uncertain significance (Feb 17, 2022)
6-1313019-C-G		not specified	Uncertain significance (Jan 21, 2025)
6-1313041-C-T		not specified	Uncertain significance (Jul 30, 2024)
6-1313053-C-T		not specified	Uncertain significance (Jul 14, 2023)
6-1313061-G-C		not specified	Uncertain significance (Aug 21, 2023)
6-1313065-C-T		not specified	Uncertain significance (Feb 26, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXQ1	protein_coding	protein_coding	ENST00000296839	1	2318

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.618	0.352	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.809	97	122	0.794	0.00000569	2393
Missense in Polyphen		46	64.342	0.71493		850
Synonymous	-0.223	58	55.9	1.04	0.00000277	904
Loss of Function	1.62	0	3.06	0.00	1.29e-7	54

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in hair follicle differentiation. {ECO:0000250}.
• Pathway: Preimplantation Embryo;EMT transition in Colorectal Cancer (Consensus)

Haploinsufficiency Scores

• pHI: 0.0818

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.262

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxq1
• Phenotype: craniofacial phenotype; homeostasis/metabolism phenotype; hematopoietic system 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); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands 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); vision/eye phenotype; digestive/alimentary phenotype; hearing/vestibular/ear 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); renal/urinary system phenotype; skeleton phenotype; immune system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; neoplasm

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;anatomical structure morphogenesis;cell differentiation;hair follicle morphogenesis
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific