HPN

hepsin, the group of Type II transmembrane serine proteases|Scavenger receptor cysteine rich domain containing

Basic information

Region (hg38): 19:35040505-35066573

Links

ENSG00000105707 ∙ NCBI:3249 ∙ OMIM:142440 ∙ HGNC:5155 ∙ Uniprot:P05981 ∙ 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 HPN gene.

• Inborn genetic diseases (10 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HPN 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			10		1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	10	0	2

Variants in HPN

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

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

Position	Type	Phenotype	Significance	ClinVar
19-35042511-C-T		not specified	Uncertain significance (Sep 06, 2022)
19-35049295-C-T		not specified	Uncertain significance (Apr 07, 2022)
19-35049296-G-A			Benign (Jul 04, 2018)
19-35049307-T-C		not specified	Uncertain significance (Aug 03, 2022)
19-35049324-G-C		not specified	Uncertain significance (Oct 05, 2023)
19-35049326-T-C		not specified	Uncertain significance (Dec 13, 2023)
19-35049505-C-T		not specified	Uncertain significance (Jan 10, 2022)
19-35059800-C-G			Benign (Jul 04, 2018)
19-35059965-A-G		not specified	Likely benign (Oct 10, 2023)
19-35059973-G-T		not specified	Uncertain significance (Oct 18, 2021)
19-35060410-G-A		not specified	Uncertain significance (Oct 13, 2023)
19-35060670-G-A		not specified	Uncertain significance (Nov 13, 2023)
19-35060710-A-T		not specified	Uncertain significance (Oct 12, 2021)
19-35060712-G-T		not specified	Uncertain significance (Aug 16, 2021)
19-35060720-C-T			Benign (May 04, 2018)
19-35065253-A-G		not specified	Uncertain significance (Aug 26, 2022)
19-35065877-G-A		not specified	Uncertain significance (Dec 18, 2023)
19-35065904-A-G		not specified	Uncertain significance (Jun 11, 2021)
19-35065905-T-G		not specified	Uncertain significance (Sep 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HPN	protein_coding	protein_coding	ENST00000262626	12	26066

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000887	125740	0	3	125743	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.79	181	263	0.689	0.0000176	2651
Missense in Polyphen		40	88.28	0.4531		908
Synonymous	0.696	104	113	0.917	0.00000828	858
Loss of Function	4.42	1	24.7	0.0404	0.00000136	247

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	0.0000529	0.0000462
European (Non-Finnish)	0.0000184	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine protease that cleaves extracellular substrates, and contributes to the proteolytic processing of growth factors, such as HGF and MST1/HGFL (PubMed:21875933, PubMed:15839837). Plays a role in cell growth and maintenance of cell morphology (PubMed:8346233, PubMed:21875933). Plays a role in the proteolytic processing of ACE2 (PubMed:24227843). Mediates the proteolytic cleavage of urinary UMOD that is required for UMOD polymerization (PubMed:26673890). {ECO:0000269|PubMed:15839837, ECO:0000269|PubMed:21875933, ECO:0000269|PubMed:24227843, ECO:0000269|PubMed:26673890, ECO:0000269|PubMed:8346233}.
• Pathway: Viral carcinogenesis - Homo sapiens (human);Signal Transduction;MET Receptor Activation;Signaling by MET;Signaling by MST1;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.262

Intolerance Scores

• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.282
• hipred: Y
• hipred_score: 0.729
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.538

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hpn
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism 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); hearing/vestibular/ear phenotype

Zebrafish Information Network

• Gene name: hpn
• Affected structure: blood coagulation, fibrin clot formation
• Phenotype tag: abnormal
• Phenotype quality: delayed

Gene ontology

• Biological process: proteolysis;regulation of cell shape;positive regulation of gene expression;negative regulation of epithelial to mesenchymal transition;positive regulation of plasminogen activation;positive regulation of cell growth;basement membrane disassembly;negative regulation of apoptotic process;positive regulation by host of viral transcription;hepatocyte growth factor receptor signaling pathway;negative regulation of epithelial cell proliferation;detection of mechanical stimulus involved in sensory perception of sound;potassium ion transmembrane transport;cochlea morphogenesis;response to thyroid hormone;pilomotor reflex;positive regulation of hepatocyte proliferation;positive regulation of thyroid hormone generation
• Cellular component: endoplasmic reticulum membrane;plasma membrane;integral component of plasma membrane;cell-cell junction;cell surface;integral component of membrane;apical plasma membrane;nuclear membrane;neuronal cell body;extracellular exosome
• Molecular function: serine-type endopeptidase activity;protein binding;peptidase activity;serine-type peptidase activity;calcium-activated potassium channel activity;serine-type exopeptidase activity