TNP2

Chr 16

transition protein 2

Also known as: TP2

NCBI Gene: 7142ENSG00000178279UniProt: Q05952

Predicted to enable zinc ion binding activity. Predicted to be involved in several processes, including penetration of zona pellucida; positive regulation of protein processing; and sperm DNA condensation. Predicted to act upstream of or within binding activity of sperm to zona pellucida and flagellated sperm motility. Predicted to be located in male germ cell nucleus. Predicted to be part of nucleosome. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

61
ClinVar variants
17
Pathogenic / LP
0.01
pLI score
0
Active trials
Clinical Summary— TNP2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.01) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
17 Pathogenic / Likely Pathogenic· 38 VUS of 61 total submissions

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.
1.78LOEUF
pLI 0.009
Z-score 0.29
OE 0.84 (0.37–1.78)
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 1.17 (0.99–1.38)
99 obs / 84.9 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.0.84 (0.37–1.78)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.17 (0.99–1.38)
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.1.49
0≤1.21.6
LoF obs/exp: 3 / 3.6Missense obs/exp: 99 / 84.9Syn Z: -2.07

ClinVar Variant Classifications

61 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic17
VUS38
Likely Benign5
Benign1
17
Pathogenic
38
VUS
5
Likely Benign
1
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
27
11
0
38
Likely Benign
0
3
1
1
5
Benign
0
0
0
1
1
Total03029261

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

View in ClinVar →

Protein Context — Lollipop Plot

TNP2 · 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
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Polymorphisms and expression levels of TNP2, SYCP3, and AZFa genes in patients with azoospermia.
Jebur MII et al.·Clin Exp Reprod Med
2023🔓 Open AccessCohort
Sequence variability of CatSper1 and TNP2 gene in indigenous and crossbred cattle in Bangladesh.
Jahan N et al.·Anim Biotechnol
2023
Correlation of Novel Single Nucleotide Polymorphisms ofUSP26, TEX15, and TNP2 Genes with Male Infertility in North West of Iran.
Ghadirkhomi E et al.·Int J Fertil Steril
2022🔓 Open Access
Search for Associations of FSHR, INHA, INHAB, PRL, TNP2 and SPEF2 Genes Polymorphisms with Semen Quality in Russian Holstein Bulls (Pilot Study).
Nikitkina E et al.·Animals (Basel)
2021🔓 Open Access
Spermatozoa retrieval in azoospermia and expression profile of JMJD1A, TNP2, and PRM2 in a subset of the Karachi population.
Amjad S et al.·Andrology
2021
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools