HPN
hepsin, the group of Type II transmembrane serine proteases|Scavenger receptor cysteine rich domain containing
Basic information
Region (hg38): 19:35040506-35066573
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
| missense | 15 | 17 | ||||
| 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 | 15 | 1 | 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) | ||
| 19-35059720-G-A | not specified | Uncertain significance (Mar 30, 2024) | ||
| 19-35059800-C-G | Benign (Jul 04, 2018) | |||
| 19-35059951-G-A | not specified | Uncertain significance (May 01, 2024) | ||
| 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:
| 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:
- 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
- loftool
- 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