HTRA3

HtrA serine peptidase 3, the group of PDZ domain containing

Basic information

Region (hg38): 4:8269754-8307098

Links

ENSG00000170801 ∙ NCBI:94031 ∙ OMIM:608785 ∙ HGNC:30406 ∙ Uniprot:P83110 ∙ 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 HTRA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTRA3 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			38		1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	1	1

Variants in HTRA3

This is a list of pathogenic ClinVar variants found in the HTRA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-8269996-G-C		not specified	Uncertain significance (Mar 19, 2024)
4-8270047-G-T		not specified	Uncertain significance (Jun 03, 2022)
4-8270072-C-G		not specified	Uncertain significance (Apr 06, 2023)
4-8270089-G-A		not specified	Uncertain significance (Jun 28, 2024)
4-8270093-G-T		not specified	Uncertain significance (Oct 12, 2022)
4-8270150-C-T		not specified	Uncertain significance (Jun 21, 2023)
4-8270155-G-A		not specified	Uncertain significance (Apr 07, 2023)
4-8270179-G-T		not specified	Uncertain significance (Mar 07, 2023)
4-8270230-G-A		not specified	Uncertain significance (Jan 24, 2023)
4-8270294-G-A		not specified	Uncertain significance (Dec 26, 2023)
4-8270311-G-A		not specified	Uncertain significance (Sep 07, 2022)
4-8270329-C-A		not specified	Uncertain significance (Mar 30, 2024)
4-8282461-G-A		not specified	Uncertain significance (Feb 16, 2023)
4-8286566-C-T		not specified	Uncertain significance (Sep 26, 2024)
4-8286583-G-A		not specified	Uncertain significance (Sep 08, 2024)
4-8286598-G-A		not specified	Uncertain significance (Jun 02, 2024)
4-8286626-G-A		not specified	Uncertain significance (Jun 05, 2024)
4-8286660-C-G		not specified	Uncertain significance (Sep 02, 2024)
4-8286672-C-T			Likely benign (Nov 01, 2024)
4-8286674-C-A		not specified	Uncertain significance (Jun 05, 2023)
4-8286674-C-T		not specified	Uncertain significance (Feb 25, 2025)
4-8286712-G-T		not specified	Uncertain significance (Jan 19, 2025)
4-8286715-T-G		not specified	Uncertain significance (Sep 16, 2021)
4-8286739-A-G		not specified	Uncertain significance (Aug 12, 2024)
4-8286766-A-G		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTRA3	protein_coding	protein_coding	ENST00000307358	9	37347

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.58e-8	0.454	125712	0	35	125747	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.496	243	266	0.914	0.0000169	2874
Missense in Polyphen		93	115.36	0.80614		1129
Synonymous	-0.178	124	122	1.02	0.00000851	960
Loss of Function	0.853	13	16.8	0.775	7.93e-7	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000297	0.000297
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000977	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.000335	0.000327
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine protease that cleaves beta-casein/CSN2 as well as several extracellular matrix (ECM) proteoglycans such as decorin/DCN, biglycan/BGN and fibronectin/FN1. Inhibits signaling mediated by TGF-beta family proteins possibly indirectly by degradation of these ECM proteoglycans (By similarity). May act as a tumor suppressor. Negatively regulates, in vitro, trophoblast invasion during placental development and may be involved in the development of the placenta in vivo. May also have a role in ovarian development, granulosa cell differentiation and luteinization (PubMed:21321049, PubMed:22229724). {ECO:0000250|UniProtKB:Q9D236, ECO:0000269|PubMed:21321049, ECO:0000269|PubMed:22229724}.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.279
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.77

Haploinsufficiency Scores

• pHI: 0.162
• hipred: N
• hipred_score: 0.276
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.362

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Htra3

Gene ontology

• Biological process: regulation of cell growth;proteolysis;negative regulation of transforming growth factor beta receptor signaling pathway;negative regulation of BMP signaling pathway
• Cellular component: extracellular region
• Molecular function: endopeptidase activity;serine-type endopeptidase activity;protein binding;insulin-like growth factor binding;serine-type peptidase activity