HGFAC

HGF activator

Basic information

Region (hg38): 4:3441968-3449486

Links

ENSG00000109758 ∙ NCBI:3083 ∙ OMIM:604552 ∙ HGNC:4894 ∙ Uniprot:Q04756 ∙ 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 HGFAC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HGFAC 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			64	5		69
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	64	7	0

Variants in HGFAC

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

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

Position	Type	Phenotype	Significance	ClinVar
4-3442038-C-T		not specified	Likely benign (May 26, 2024)
4-3442041-C-G		not specified	Uncertain significance (Oct 20, 2023)
4-3442062-C-T		not specified	Uncertain significance (Feb 17, 2024)
4-3442065-C-T		not specified	Uncertain significance (Mar 22, 2023)
4-3442075-T-A		not specified	Uncertain significance (Aug 16, 2021)
4-3442739-C-T		not specified	Uncertain significance (Feb 01, 2023)
4-3442766-C-T		not specified	Likely benign (Dec 27, 2022)
4-3442832-C-T		not specified	Uncertain significance (Feb 21, 2024)
4-3442861-C-T		not specified	Uncertain significance (Dec 07, 2023)
4-3442865-C-G			Likely benign (Apr 01, 2023)
4-3442871-C-G		not specified	Uncertain significance (Jun 03, 2024)
4-3443088-C-T		not specified	Uncertain significance (Jun 18, 2021)
4-3443089-G-A		not specified	Uncertain significance (Sep 12, 2023)
4-3443094-G-A		not specified	Uncertain significance (Jan 23, 2024)
4-3443112-G-C		not specified	Uncertain significance (Jun 28, 2024)
4-3443122-C-T		not specified	Uncertain significance (Feb 03, 2022)
4-3443127-G-A		not specified	Uncertain significance (Aug 21, 2023)
4-3443348-A-C		not specified	Uncertain significance (Jul 16, 2024)
4-3443349-C-T		not specified	Uncertain significance (Mar 20, 2023)
4-3443365-C-A		not specified	Uncertain significance (Oct 16, 2023)
4-3443366-C-T		not specified	Uncertain significance (Dec 06, 2022)
4-3443403-C-T		not specified	Uncertain significance (May 02, 2024)
4-3444041-GCCCTGGATCCCTGTGC-G			Likely benign (Oct 01, 2023)
4-3444060-C-G		not specified	Uncertain significance (Jun 17, 2022)
4-3444075-A-G		not specified	Uncertain significance (Aug 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HGFAC	protein_coding	protein_coding	ENST00000382774	14	7598

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.98e-8	0.968	124697	5	934	125636	0.00374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.580	458	424	1.08	0.0000297	4129
Missense in Polyphen		199	178.61	1.1142		1723
Synonymous	-1.98	230	195	1.18	0.0000154	1350
Loss of Function	2.09	17	29.2	0.583	0.00000133	330

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00509	0.00506
Ashkenazi Jewish	0.00709	0.00617
East Asian	0.00344	0.00332
Finnish	0.00460	0.00449
European (Non-Finnish)	0.00312	0.00290
Middle Eastern	0.00344	0.00332
South Asian	0.00632	0.00577
Other	0.00976	0.00901

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Activates hepatocyte growth factor (HGF) by converting it from a single chain to a heterodimeric form.
• Pathway: Signal Transduction;MET Receptor Activation;Signaling by MET;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.144
• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.67

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.300
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.250

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hgfac
• Phenotype: homeostasis/metabolism phenotype; digestive/alimentary phenotype; 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)

Gene ontology

• Biological process: proteolysis
• Cellular component: extracellular region;extracellular space;rough endoplasmic reticulum;cytosol
• Molecular function: serine-type endopeptidase activity;serine-type peptidase activity