GeneBe

PCSK5

proprotein convertase subtilisin/kexin type 5, the group of Proprotein convertase subtilisin/kexin family

Basic information

Region (hg38): 9:75890644-76362975

Links

ENSG00000099139 ∙ NCBI:5125 ∙ OMIM:600488 ∙ HGNC:8747 ∙ Uniprot:Q92824 ∙ 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 PCSK5 gene.

  • not_specified (91 variants)
  • not_provided (22 variants)
  • PCSK5-related_disorder (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCSK5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001372043.1. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
9
clinvar
9
clinvar
 21
missense
89
clinvar
7
clinvar
6
clinvar
 102
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 93 16 15
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PCSK5protein_codingprotein_codingENST00000545128 37471696
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
2.54e-121.0012561301351257480.000537
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.578401.08e+30.7800.000061012320
Missense in Polyphen206423.920.485944761
Synonymous0.6233984140.9610.00002643274
Loss of Function5.79391020.3820.000005141249

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008530.000783
Ashkenazi Jewish0.001310.00129
East Asian0.001800.00174
Finnish0.00009260.0000924
European (Non-Finnish)0.0005930.000554
Middle Eastern0.001800.00174
South Asian0.0002330.000196
Other0.0001680.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Serine endoprotease that processes various proproteins by cleavage at paired basic amino acids, recognizing the RXXX[KR]R consensus motif. Likely functions in the constitutive and regulated secretory pathways. Plays an essential role in pregnancy establishment by proteolytic activation of a number of important factors such as BMP2, CALD1 and alpha-integrins. {ECO:0000269|PubMed:19764806, ECO:0000269|PubMed:20555025, ECO:0000269|PubMed:22740495}.;
Pathway
Signal Transduction;Transport of small molecules;NGF processing;Expression and Processing of Neurotrophins;Signaling by NTRKs;Assembly of active LPL and LIPC lipase complexes;Plasma lipoprotein assembly, remodeling, and clearance;Plasma lipoprotein remodeling;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

pRec
0.242

Intolerance Scores

loftool
0.825
rvis_EVS
2.84
rvis_percentile_EVS
99.1

Haploinsufficiency Scores

pHI
0.122
hipred
Y
hipred_score
0.639
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.774

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Pcsk5
Phenotype
mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); respiratory system phenotype; embryo phenotype; skeleton phenotype; renal/urinary system phenotype; immune system 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); limbs/digits/tail phenotype; digestive/alimentary phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; cellular phenotype; craniofacial phenotype;

Zebrafish Information Network

Gene name
pcsk5a
Affected structure
lateral line
Phenotype tag
abnormal
Phenotype quality
morphology

Gene ontology

Biological process
kidney development;renin secretion into blood stream;cardiac septum development;signal peptide processing;cell-cell signaling;determination of left/right symmetry;heart development;embryo implantation;anterior/posterior pattern specification;protein processing;peptide hormone processing;viral life cycle;respiratory tube development;limb morphogenesis;cytokine biosynthetic process;peptide biosynthetic process;embryonic digestive tract development;embryonic skeletal system development;regulation of lipoprotein lipase activity;coronary vasculature development
Cellular component
extracellular region;extracellular space;Golgi apparatus;Golgi lumen;trans-Golgi network;membrane;integral component of membrane;secretory granule;integral component of Golgi membrane
Molecular function
endopeptidase activity;serine-type endopeptidase activity;protein binding;peptidase activity;peptide binding