PRM1

Chr 16

protamine 1

Also known as: CT94.1, P1

NCBI Gene: 5619ENSG00000175646UniProt: P04553

Predicted to enable DNA binding activity. Predicted to be involved in chromosome organization and spermatogenesis. Predicted to act upstream of or within nucleus organization and spermatid development. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

47
ClinVar variants
17
Pathogenic / LP
0.03
pLI score
1
Active trials
Clinical Summary— PRM1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.03) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
17 Pathogenic / Likely Pathogenic· 27 VUS of 47 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
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.
1.87LOEUF
pLI 0.027
Z-score 0.07
OE 0.95 (0.35–1.87)
Tolerant

Highly tolerant — LoF variants common in population

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.
-0.54Z-score
OE missense 1.25 (0.98–1.60)
45 obs / 36.0 exp
Tolerant

Tolerant to missense variation

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.0.95 (0.35–1.87)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.25 (0.98–1.60)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.63
0≤1.21.6
LoF obs/exp: 2 / 2.1Missense obs/exp: 45 / 36.0Syn Z: -1.60

ClinVar Variant Classifications

47 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic17
VUS27
Likely Benign1
Benign2
17
Pathogenic
27
VUS
1
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
17
0
17
Likely Pathogenic
0
0
0
0
0
VUS
0
15
12
0
27
Likely Benign
0
0
1
0
1
Benign
0
0
1
1
2
Total01531147

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

View in ClinVar →

Protein Context — Lollipop Plot

PRM1 · 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

OMIM
SPERM PROTAMINE P1; PRM1
MIM #182880 · *
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Protamine expression in somatic cells condenses chromatin and disrupts transcription without altering DNA methylation.
Puri D et al.·Epigenetics Chromatin
2025
Impact of tobacco smoking in association with H2BFWT, PRM1 and PRM2 genes variants on male infertility.
Amor H et al.·Andrologia
2022
Protamine 1 as a secreted colorectal cancer-specific antigen facilitating G1/S phase transition under nutrient stress conditions.
Ren S et al.·Cell Oncol (Dordr)
2023
PRM1 variant rs35576928 (Arg>Ser) is associated with defective spermatogenesis in the Chinese Han population.
He XJ et al.·Reprod Biomed Online
2012
Identification of the PRM1 gene mutations in oligoasthenoteratozoospermic men.
Nasirshalal M et al.·Andrologia
2020
Impact of protamine I on colon cancer proliferation, invasion, migration, diagnosis and prognosis.
Chen Z et al.·Biol Chem
2018
Non-major histocompatibility complex rheumatoid arthritis susceptibility genes.
Kunz M et al.·Crit Rev Immunol
2011Review
Loss of the cleaved-protamine 2 domain leads to incomplete histone-to-protamine exchange and infertility in mice.
Arévalo L et al.·PLoS Genet
2022
Evaluation of cell-free seminal mRNA for the diagnosis of obstruction as the cause of azoospermia in infertile men: A prospective cohort study.
Goel R et al.·Andrologia
2022Cohort
Development and validation of a deep learning model based on cascade mask regional convolutional neural network to noninvasively and accurately identify human round spermatids.
Sun Y et al.·J Adv Res
2026Functional
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
PRM1 modulates proliferation, apoptosis, and testosterone synthesis in bovine Leydig cells.
Wang X et al.·Anim Reprod Sci
2025
Evaluation of TNP1 and PRM1 gene expression in male infertility patients with low or high sperm DNA fragmentation.
Şahin Y et al.·J Turk Ger Gynecol Assoc
2025🔓 Open AccessCohort
Sperm RNA quantity and PRM1, PRM2 , and TH2B transcript levels reflect sperm characteristics and early embryonic development.
Ozsait-Selcuk B et al.·Asian J Androl
2025🔓 Open Access
CircANXA4 (hsa_circ_0055087) regulates the miR-1256/PRM1 axis to promote tumor progression in colorectal cancer.
Liu G et al.·Noncoding RNA Res
2024🔓 Open Access
Immunization with a heat-killed prm1 deletion strain protects the host from Cryptococcus neoformans infection.
Li C et al.·Emerg Microbes Infect
2023🔓 Open Access
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Infertility, MaleGene AbnormalitySterility, Male

Spermatogonial Differentiation Via Testicular Organoid

RECRUITING
NCT06841861Phase PHASE1, PHASE2CellARTs Inc.Started 2024-03-28
Stem cellGenetic ScreeningGenetic Reprogramming

External Resources

Links to major genomics databases and tools