PCSK1

Chr 5AR

proprotein convertase subtilisin/kexin type 1

Also known as: BMIQ12, NEC1, PC1, PC1/3, PC3, SPC3

This gene encodes a member of the subtilisin-like proprotein convertase family, which includes proteases that process protein and peptide precursors trafficking through regulated or constitutive branches of the secretory pathway. The encoded protein undergoes an initial autocatalytic processing event in the ER to generate a heterodimer which exits the ER and sorts to subcellular compartments where a second autocatalytic even takes place and the catalytic activity is acquired. The protease is packaged into and activated in dense core secretory granules and expressed in the neuroendocrine system and brain. This gene encodes one of the seven basic amino acid-specific members which cleave their substrates at single or paired basic residues. It functions in the proteolytic activation of polypeptide hormones and neuropeptides precursors. Mutations in this gene have been associated with susceptibility to obesity and proprotein convertase 1/3 deficiency. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene [provided by RefSeq, Jan 2014]

Primary Disease Associations & Inheritance

{Obesity, susceptibility to, BMIQ12}MIM #612362
Endocrinopathy due to proprotein convertase 1/3 deficiencyMIM #600955
AR
481
ClinVar variants
61
Pathogenic / LP
0.00
pLI score
8
Active trials
Clinical SummaryPCSK1
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
61 Pathogenic / Likely Pathogenic· 229 VUS of 481 total submissions
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Clinical Trials
8 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.73LOEUF
pLI 0.000
Z-score 2.94
OE 0.51 (0.360.73)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.47Z-score
OE missense 0.80 (0.730.87)
328 obs / 412.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.51 (0.360.73)
00.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.80 (0.730.87)
00.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.05
01.21.6
LoF obs/exp: 21 / 41.4Missense obs/exp: 328 / 412.0Syn Z: -0.51

ClinVar Variant Classifications

481 submitted variants in ClinVar

Classification Summary

Pathogenic35
Likely Pathogenic26
VUS229
Likely Benign145
Benign33
Conflicting13
35
Pathogenic
26
Likely Pathogenic
229
VUS
145
Likely Benign
33
Benign
13
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
4
3
28
0
35
Likely Pathogenic
9
9
8
0
26
VUS
1
179
43
6
229
Likely Benign
0
8
43
94
145
Benign
0
2
29
2
33
Conflicting
13
Total14201151102481

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

PCSK1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

{Obesity, susceptibility to, BMIQ12}

MIM #612362

Molecular basis of disorder known

Endocrinopathy due to proprotein convertase 1/3 deficiency

MIM #600955

Molecular basis of disorder known

Autosomal recessive
📖
GeneReview available — PCSK1
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Genetics of Obesity in Humans: A Clinical Review.
Mahmoud R et al.·Int J Mol Sci
2022Review
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

Obesity and Obesity-related Medical ConditionsCardiovascular RiskGenetics

Cardiometabolic Risk of Obese Subjects: Cross-sectional Study

RECRUITING
NCT06714058IRCCS Azienda Ospedaliero-Universitaria di BolognaStarted 2024-11-30
Obesity

Intensive Weight Loss Intervention Versus Usual Care for Adults With Obesity

ACTIVE NOT RECRUITING
NCT06321432Phase NACarsten DirksenStarted 2024-06-05
Intensive weight loss interventionUsual care
Monogenic Obesity

Efficacy of Semaglutide s.c. Once-weekly on Weight Loss and Management in Adolescents With Monogenic Obesity in Clinical Practice

RECRUITING
NCT07302802Prof. Dr. Martin WabitschStarted 2025-12-01
Semaglutide (administered by PDS290 pen-injector)
Morbid ObesityBariatric SurgeryTelerehabilitation

Exercise to Fight Obesity

RECRUITING
NCT06934681Phase NAInstituto de Investigacion Sanitaria La FeStarted 2025-05-19
Usual Care GroupControlled exercise with telerehabilitation
Obesity, ChildhoodHyperphagiaRetinopathy

Early Genetic Identification of Obesity

ACTIVE NOT RECRUITING
NCT06239064Rolfs Consulting und Verwaltungs-GmbH (RCV)Started 2024-01-24
Genetic testing via blood collection
Obesity

Intensive Weight Loss Intervention Versus Bariatric Surgery for Adults With Severe and Complex Obesity: the LightBAR Randomised Trial

RECRUITING
NCT06309238Phase NACarsten DirksenStarted 2024-05-08
Intensive weight loss interventionBariatric surgery
ObesityGenetic Obesity

EMANATE: A Study of Setmelanotide in Patients With Specific Gene Variants in the MC4R Pathway

ACTIVE NOT RECRUITING
NCT05093634Phase PHASE3Rhythm Pharmaceuticals, Inc.Started 2021-12-10
SetmelanotidePlacebo
Obesity

Intensive Weight Loss Intervention Versus Usual Care for Adults With Severe and Complex Obesity

RECRUITING
NCT06321458Phase NACarsten DirksenStarted 2024-04-29
Intensive weight loss interventionUsual care