FOXA3

forkhead box A3, the group of Forkhead boxes

Basic information

Region (hg38): 19:45863989-45873797

Previous symbols: [ "HNF3G" ]

Links

ENSG00000170608 ∙ NCBI:3171 ∙ OMIM:602295 ∙ HGNC:5023 ∙ Uniprot:P55318 ∙ 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 FOXA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXA3 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	3	5
missense			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	14	5	3

Variants in FOXA3

This is a list of pathogenic ClinVar variants found in the FOXA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-45864448-G-C		FOXA3-related disorder	Likely benign (Aug 29, 2019)
19-45872102-A-C		not specified	Uncertain significance (May 23, 2023)
19-45872114-C-A		not specified	Uncertain significance (Sep 21, 2021)
19-45872255-A-C		not specified	Uncertain significance (Sep 26, 2024)
19-45872258-G-A		not specified	Uncertain significance (Dec 20, 2023)
19-45872264-A-G		not specified	Likely benign (Feb 03, 2022)
19-45872271-G-A		not specified	Uncertain significance (Feb 21, 2024)
19-45872292-G-C		not specified	Uncertain significance (Oct 06, 2022)
19-45872350-C-T		FOXA3-related disorder	Benign (May 15, 2019)
19-45872383-C-G		not specified	Uncertain significance (Sep 16, 2021)
19-45872403-C-T		not specified	Uncertain significance (Aug 05, 2024)
19-45872483-C-A		not specified	Uncertain significance (Nov 12, 2021)
19-45872521-C-T		FOXA3-related disorder	Benign (Nov 06, 2019)
19-45872544-G-C		not specified	Uncertain significance (Feb 06, 2024)
19-45872716-T-C		FOXA3-related disorder	Likely benign (Jul 30, 2019)
19-45872721-C-T		not specified	Uncertain significance (Sep 30, 2021)
19-45872730-C-G		not specified	Uncertain significance (Mar 02, 2023)
19-45872754-C-T		not specified	Uncertain significance (Jun 22, 2021)
19-45872829-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-45872879-C-G		FOXA3-related disorder	Likely benign (Sep 20, 2022)
19-45872891-G-A		not specified	Uncertain significance (May 17, 2023)
19-45872934-T-C		not specified	Uncertain significance (Nov 28, 2024)
19-45872959-C-A		FOXA3-related disorder	Benign (Feb 22, 2019)
19-45872968-C-T		FOXA3-related disorder	Likely benign (Jun 25, 2019)
19-45872973-G-A		not specified	Uncertain significance (Apr 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXA3	protein_coding	protein_coding	ENST00000302177	2	9809

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.733	0.265	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.243	207	217	0.954	0.0000136	2209
Missense in Polyphen		33	53.51	0.61671		515
Synonymous	-0.751	107	97.6	1.10	0.00000658	774
Loss of Function	2.42	1	8.68	0.115	3.71e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.0000741	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000985	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that is thought to act as a 'pioneer' factor opening the compacted chromatin for other proteins through interactions with nucleosomal core histones and thereby replacing linker histones at target enhancer and/or promoter sites (By similarity). Originally described as a transcription activator for a number of liver genes such as AFP, albumin, tyrosine aminotransferase, PEPCK, etc. Interacts with the cis-acting regulatory regions of these genes. Involved in glucose homeostasis; binds to and activates transcription from the G6PC promoter. Binds to the CYP3A4 promoter and activates its transcription in cooperation with CEBPA. Binds to the CYP3A7 promoter together with members of the CTF/NF-I family. Involved in regulation of neuronal-specific transcription. May be involved in regulation of spermatogenesis. {ECO:0000250, ECO:0000269|PubMed:12695546}.
• Pathway: Maturity onset diabetes of the young - Homo sapiens (human);FOXA1 transcription factor network;FOXA2 and FOXA3 transcription factor networks (Consensus)

Recessive Scores

• pRec: 0.245

Intolerance Scores

• loftool: 0.0307
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.09

Haploinsufficiency Scores

• pHI: 0.969
• hipred: N
• hipred_score: 0.479
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.919

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxa3
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: foxa3
• Affected structure: goblet cell
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Biological process: cellular glucose homeostasis;chromatin organization;regulation of transcription by RNA polymerase II;multicellular organism development;spermatogenesis;cellular response to starvation;anatomical structure morphogenesis;cell differentiation;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;actin cytoskeleton
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription factor binding;protein domain specific binding;sequence-specific DNA binding;transcription regulatory region DNA binding