JPT2

Chr 16

Jupiter microtubule associated homolog 2

Also known as: C16orf34, HN1L, L11

NCBI Gene: 90861ENSG00000206053UniProt: Q9H910

Involved in endocytosis involved in viral entry into host cell and regulation of calcium-mediated signaling. Located in cytosol; nucleus; and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

101
ClinVar variants
41
Pathogenic / LP
0.23
pLI score
0
Active trials
Clinical Summary— JPT2
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.27) despite low pLI — interpret in context.
📋
ClinVar Variants
41 Pathogenic / Likely Pathogenic· 57 VUS of 101 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.
0.86LOEUF
pLI 0.233
Z-score 1.82
OE 0.27 (0.11–0.86)
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.
0.45Z-score
OE missense 0.88 (0.75–1.04)
98 obs / 111.3 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.0.27 (0.11–0.86)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.88 (0.75–1.04)
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.0.83
0≤1.21.6
LoF obs/exp: 2 / 7.3Missense obs/exp: 98 / 111.3Syn Z: 0.85

ClinVar Variant Classifications

101 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic40
Likely Pathogenic1
VUS57
Likely Benign3
40
Pathogenic
1
Likely Pathogenic
57
VUS
3
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
40
0
40
Likely Pathogenic
0
0
1
0
1
VUS
0
38
19
0
57
Likely Benign
0
3
0
0
3
Benign
0
0
0
0
0
Total041600101

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

View in ClinVar →

Protein Context — Lollipop Plot

JPT2 · 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
JPT2 Affects Trophoblast Functions and Macrophage Polarization and Metabolism, and Acts as a Potential Therapeutic Target for Recurrent Spontaneous Abortion.
Chen X et al.·Adv Sci (Weinh)
2024
MASTER-NAADP: a membrane permeable precursor of the Ca(2+) mobilizing second messenger NAADP.
Krukenberg S et al.·Nat Commun
2024
TPCs: FROM PLANT TO HUMAN.
Klingl YE et al.·Physiol Rev
2025Review
Convergent activation of two-pore channels mediated by the NAADP-binding proteins JPT2 and LSM12.
Gunaratne GS et al.·Sci Signal
2023
NAADP-binding proteins - Linking NAADP signaling to cancer and immunity.
Heßling LD et al.·Biochim Biophys Acta Mol Cell Res
2023Review
HN1L/JPT2: A signaling protein that connects NAADP generation to Ca(2+) microdomain formation.
Roggenkamp HG et al.·Sci Signal
2021
NAADP: From Discovery to Mechanism.
Walseth TF et al.·Front Immunol
2021Review
JPT2 in subclinical hypothyroidism-related miscarriage as a transcription co-factor: involvement of LEPR/STAT3 activation.
Zhou YY et al.·J Endocrinol Invest
2024
Systematic identification of microtubule lumen proteins reveals a taxane-sensitive luminal resident JPT2 regulating MEC17 accessibility.
Shao J et al.·Proc Natl Acad Sci U S A
2026
Imaging Initial Ca2+ Microdomains in Primary T Cells.
Gerlach F et al.·J Vis Exp
2024
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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