HNF4G

hepatocyte nuclear factor 4 gamma, the group of Hepatocyte nuclear factor 4 family

Basic information

Region (hg38): 8:75407913-75566834

Links

ENSG00000164749 ∙ NCBI:3174 ∙ OMIM:605966 ∙ HGNC:5026 ∙ Uniprot:Q14541 ∙ 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 HNF4G gene.

• Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNF4G 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						0
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in HNF4G

This is a list of pathogenic ClinVar variants found in the HNF4G region.

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

Position	Type	Phenotype	Significance	ClinVar
8-75540032-T-G		not specified	Uncertain significance (Mar 07, 2023)
8-75540057-T-C		not specified	Uncertain significance (Mar 05, 2024)
8-75543973-C-A		not specified	Uncertain significance (May 22, 2023)
8-75547594-C-T		not specified	Uncertain significance (Mar 29, 2023)
8-75551461-C-A		not specified	Uncertain significance (Dec 20, 2023)
8-75551483-C-T		not specified	Uncertain significance (Jul 26, 2021)
8-75553081-G-A		not specified	Uncertain significance (Jul 15, 2021)
8-75553120-A-G		not specified	Uncertain significance (Aug 17, 2021)
8-75553179-A-C		not specified	Uncertain significance (Apr 07, 2023)
8-75553183-C-T		not specified	Uncertain significance (Dec 02, 2022)
8-75556011-G-C		not specified	Uncertain significance (Jul 26, 2022)
8-75558566-G-A		not specified	Uncertain significance (Jan 10, 2022)
8-75558575-A-G		not specified	Uncertain significance (Feb 23, 2023)
8-75558820-T-A		not specified	Uncertain significance (Jul 08, 2022)
8-75558857-A-G		not specified	Uncertain significance (Jun 16, 2023)
8-75558935-A-G		not specified	Uncertain significance (Jun 09, 2022)
8-75558960-T-C		not specified	Uncertain significance (Oct 26, 2022)
8-75558970-A-C		not specified	Uncertain significance (Jun 12, 2023)
8-75559001-A-G		not specified	Uncertain significance (Dec 03, 2021)
8-75560353-A-G		not specified	Uncertain significance (Dec 19, 2022)
8-75564008-A-G		not specified	Uncertain significance (Mar 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HNF4G	protein_coding	protein_coding	ENST00000396423	10	158930

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0707	0.929	125685	0	49	125734	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.597	222	248	0.893	0.0000131	2944
Missense in Polyphen		51	84.963	0.60026		994
Synonymous	-1.06	96	83.7	1.15	0.00000431	810
Loss of Function	3.05	6	21.1	0.284	9.57e-7	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000300	0.000299
Middle Eastern	0.0000544	0.0000544
South Asian	0.000361	0.000359
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor. Has a lower transcription activation potential than HNF4-alpha.
• Pathway: Maturity onset diabetes of the young - Homo sapiens (human);NHR;Gene expression (Transcription);Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.228

Intolerance Scores

• loftool: 0.214
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.611
• hipred: Y
• hipred_score: 0.741
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hnf4g
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;intracellular receptor signaling pathway;steroid hormone mediated signaling pathway;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleoplasm
• Molecular function: 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;steroid hormone receptor activity;nuclear receptor activity;zinc ion binding