HPR

haptoglobin-related protein, the group of Sushi domain containing

Basic information

Region (hg38): 16:72063148-72077246

Links

ENSG00000261701 ∙ NCBI:3250 ∙ OMIM:140210 ∙ HGNC:5156 ∙ Uniprot:P00739 ∙ 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 HPR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HPR 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					3	3
missense			31	8	1	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	8	4

Variants in HPR

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

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

Position	Type	Phenotype	Significance	ClinVar
16-72074289-C-G		not specified	Uncertain significance (Oct 06, 2021)
16-72074293-T-G		not specified	Likely benign (Oct 06, 2021)
16-72074296-C-A		not specified	Uncertain significance (Aug 28, 2021)
16-72074301-C-A		not specified	Uncertain significance (Jan 10, 2023)
16-72074307-G-A		not specified	Uncertain significance (Jan 29, 2024)
16-72074311-T-C		not specified	Uncertain significance (Sep 16, 2021)
16-72074335-T-C		not specified	Likely benign (Sep 01, 2021)
16-72074337-T-G		not specified	Likely benign (Sep 01, 2021)
16-72074340-C-T		not specified	Uncertain significance (Sep 14, 2021)
16-72074365-G-A		not specified	Likely benign (Apr 28, 2022)
16-72074365-G-C		not specified	Uncertain significance (Oct 21, 2021)
16-72074370-C-T		not specified	Uncertain significance (Jun 28, 2024)
16-72074371-G-A		not specified	Uncertain significance (Oct 06, 2022)
16-72076321-A-G		not specified	Uncertain significance (Mar 24, 2023)
16-72076332-C-G		not specified	Likely benign (Oct 26, 2021)
16-72076342-G-A		not specified	Uncertain significance (Apr 06, 2024)
16-72076424-G-T			Benign (Jul 31, 2018)
16-72076446-T-C		not specified	Uncertain significance (May 10, 2024)
16-72076477-T-C		not specified	Uncertain significance (Jan 23, 2024)
16-72076479-A-C		not specified	Uncertain significance (Aug 04, 2021)
16-72076505-A-T		not specified	Uncertain significance (Dec 15, 2022)
16-72076510-T-C		not specified	Uncertain significance (Jul 13, 2021)
16-72076568-G-T			Benign (Jul 29, 2018)
16-72076578-C-G		not specified	Uncertain significance (Dec 30, 2023)
16-72076587-C-T		not specified	Uncertain significance (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HPR	protein_coding	protein_coding	ENST00000540303	5	22624

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.46e-10	0.0648	124654	1	168	124823	0.000677

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.52	243	185	1.31	0.0000105	2258
Missense in Polyphen		74	67.883	1.0901		793
Synonymous	-1.17	89	76.0	1.17	0.00000487	671
Loss of Function	-0.108	14	13.6	1.03	6.88e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000454	0.000454
Ashkenazi Jewish	0.000696	0.000695
East Asian	0.00301	0.00295
Finnish	0.000186	0.000186
European (Non-Finnish)	0.000444	0.000441
Middle Eastern	0.00301	0.00295
South Asian	0.00128	0.00128
Other	0.000670	0.000660

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Primate-specific plasma protein associated with apolipoprotein L-I (apoL-I)-containing high-density lipoprotein (HDL). This HDL particle, termed trypanosome lytic factor-1 (TLF- 1), mediates human innate immune protection against many species of African trypanosomes. Binds hemoglobin with high affinity and may contribute to the clearance of cell-free hemoglobin to allow hepatic recycling of heme iron. {ECO:0000269|PubMed:16778136}.
• Pathway: African trypanosomiasis - Homo sapiens (human);Vesicle-mediated transport;Scavenging of heme from plasma;Binding and Uptake of Ligands by Scavenger Receptors (Consensus)

Recessive Scores

• pRec: 0.841

Intolerance Scores

• loftool: 0.348
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.51

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Gene ontology

• Biological process: acute inflammatory response;proteolysis;receptor-mediated endocytosis;response to organic substance;positive regulation of cell death
• Cellular component: extracellular region;extracellular space;spherical high-density lipoprotein particle;extracellular exosome;blood microparticle
• Molecular function: serine-type endopeptidase activity;hemoglobin binding