SERPINA5

serpin family A member 5, the group of Serpin peptidase inhibitors

Basic information

Region (hg38): 14:94561441-94593118

Previous symbols: [ "PLANH3", "PCI" ]

Links

ENSG00000188488 ∙ NCBI:5104 ∙ OMIM:601841 ∙ HGNC:8723 ∙ Uniprot:P05154 ∙ 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 SERPINA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERPINA5 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			31	2	1	34
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	2	2

Variants in SERPINA5

This is a list of pathogenic ClinVar variants found in the SERPINA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-94563552-G-A		not specified	Uncertain significance (Dec 04, 2023)
14-94563681-G-A		not specified	Uncertain significance (Mar 21, 2023)
14-94563681-G-T		not specified	Uncertain significance (Sep 20, 2023)
14-94563717-C-T		not specified	Uncertain significance (Jan 03, 2022)
14-94563753-C-A		not specified	Uncertain significance (Feb 28, 2023)
14-94563775-G-A		not specified	Uncertain significance (Dec 04, 2023)
14-94563822-G-C		not specified	Uncertain significance (Jan 23, 2024)
14-94563825-T-A		not specified	Uncertain significance (Oct 10, 2023)
14-94563828-G-T		not specified	Uncertain significance (Mar 20, 2024)
14-94563841-G-A		not specified	Uncertain significance (Jun 22, 2023)
14-94563868-A-G		not specified	Likely benign (Oct 05, 2023)
14-94563892-C-A		not specified	Uncertain significance (Sep 07, 2022)
14-94563894-C-T			Benign (Apr 20, 2018)
14-94563897-G-A		not specified	Likely benign (Oct 12, 2021)
14-94563901-G-C		not specified	Uncertain significance (May 14, 2024)
14-94563933-T-C		not specified	Likely benign (Dec 21, 2022)
14-94563952-A-G		not specified	Uncertain significance (Jan 26, 2022)
14-94563953-T-A		not specified	Uncertain significance (Jan 29, 2024)
14-94563957-A-G		not specified	Uncertain significance (Feb 11, 2022)
14-94563964-C-A		not specified	Uncertain significance (Feb 15, 2023)
14-94563979-A-G		not specified	Uncertain significance (Dec 19, 2022)
14-94564002-G-A		not specified	Uncertain significance (Mar 23, 2022)
14-94564020-C-G		not specified	Uncertain significance (Jan 24, 2024)
14-94567031-G-C		not specified	Uncertain significance (Jun 22, 2023)
14-94567044-C-T		not specified	Uncertain significance (Jun 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERPINA5	protein_coding	protein_coding	ENST00000329597	4	31679

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.24e-9	0.0731	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.24	289	236	1.23	0.0000132	2693
Missense in Polyphen		90	76.153	1.1818		934
Synonymous	-1.69	121	99.6	1.21	0.00000602	793
Loss of Function	-0.296	12	10.9	1.10	4.64e-7	132

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000284	0.000284
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000888	0.0000879
Middle Eastern	0.0000545	0.0000544
South Asian	0.000104	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Heparin-dependent serine protease inhibitor acting in body fluids and secretions. Inactivates serine proteases by binding irreversibly to their serine activation site. Involved in the regulation of intravascular and extravascular proteolytic activities. Plays hemostatic roles in the blood plasma. Acts as a procoagulant and proinflammatory factor by inhibiting the anticoagulant activated protein C factor as well as the generation of activated protein C factor by the thrombin/thrombomodulin complex. Acts as an anticoagulant factor by inhibiting blood coagulation factors like prothrombin, factor XI, factor Xa, plasma kallikrein and fibrinolytic enzymes such as tissue- and urinary- type plasminogen activators. In seminal plasma, inactivates several serine proteases implicated in the reproductive system. Inhibits the serpin acrosin; indirectly protects component of the male genital tract from being degraded by excessive released acrosin. Inhibits tissue-and urinary-type plasminogen activator, prostate-specific antigen and kallikrein activities; has a control on the sperm motility and fertilization. Inhibits the activated protein C-catalyzed degradation of SEMG1 and SEMG2; regulates the degradation of semenogelin during the process of transfer of spermatozoa from the male reproductive tract into the female tract. In urine, inhibits urinary-type plasminogen activator and kallikrein activities. Inactivates membrane-anchored serine proteases activities such as MPRSS7 and TMPRSS11E. Inhibits urinary-type plasminogen activator-dependent tumor cell invasion and metastasis. May also play a non-inhibitory role in seminal plasma and urine as a hydrophobic hormone carrier by its binding to retinoic acid. {ECO:0000269|PubMed:10340997, ECO:0000269|PubMed:11722589, ECO:0000269|PubMed:14696115, ECO:0000269|PubMed:15140131, ECO:0000269|PubMed:15328353, ECO:0000269|PubMed:15853774, ECO:0000269|PubMed:1725227, ECO:0000269|PubMed:18467335, ECO:0000269|PubMed:2844223, ECO:0000269|PubMed:3501295, ECO:0000269|PubMed:6323392, ECO:0000269|PubMed:7521127, ECO:0000269|PubMed:7548057, ECO:0000269|PubMed:8536714, ECO:0000269|PubMed:8665956, ECO:0000269|PubMed:9473218, ECO:0000269|PubMed:9510955, ECO:0000269|PubMed:9556620}.
• Pathway: Complement and coagulation cascades - Homo sapiens (human);Dengue-2 Interactions with Complement and Coagulation Cascades;Complement and Coagulation Cascades;Intrinsic Pathway of Fibrin Clot Formation;Hemostasis;Common Pathway of Fibrin Clot Formation;Formation of Fibrin Clot (Clotting Cascade) (Consensus)

Recessive Scores

• pRec: 0.314

Intolerance Scores

• loftool: 0.0590
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.53

Haploinsufficiency Scores

• pHI: 0.233
• hipred: N
• hipred_score: 0.213
• ghis: 0.377

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.572

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Serpina5
• Phenotype: endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: lipid transport;spermatogenesis;fusion of sperm to egg plasma membrane involved in single fertilization;blood coagulation;negative regulation of endopeptidase activity;negative regulation of hydrolase activity;seminal vesicle development
• Cellular component: acrosomal membrane;extracellular region;extracellular space;external side of plasma membrane;membrane;platelet alpha granule;platelet dense tubular network;protein-containing complex;protein C inhibitor-TMPRSS7 complex;protein C inhibitor-TMPRSS11E complex;protein C inhibitor-PLAT complex;protein C inhibitor-PLAU complex;protein C inhibitor-thrombin complex;protein C inhibitor-KLK3 complex;protein C inhibitor-plasma kallikrein complex;collagen-containing extracellular matrix;extracellular exosome;protein C inhibitor-coagulation factor V complex;protein C inhibitor-coagulation factor Xa complex;protein C inhibitor-coagulation factor XI complex
• Molecular function: retinoic acid binding;protease binding;serine-type endopeptidase inhibitor activity;protein binding;glycosaminoglycan binding;heparin binding;phosphatidylcholine binding;acrosin binding