JPT2

Chr 16

Jupiter microtubule associated homolog 2

Also known as: C16orf34, HN1L, L11

NCBI Gene: 90861 ENSG00000206053 UniProt: Q9H910

The protein binds nicotinic acid adenine dinucleotide phosphate (NAADP) and enables NAADP-evoked intracellular calcium release by conferring NAADP sensitivity to two pore channels and activating calcium release from the endoplasmic reticulum through ryanodine receptors. Mutations in JPT2 cause autosomal recessive developmental and epileptic encephalopathy with movement abnormalities, characterized by early-onset seizures, developmental delay, and movement disorders affecting the central nervous system.

ResearchSummary from RefSeq, UniProt

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]

ResearchGenerating clinical summary…

LOEUF 0.86

Clinical Summary— JPT2

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Population Constraint (gnomAD)

Constrained for loss-of-function variants (OE-LoF 0.27) despite low pLI — interpret in context.

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ClinVar Variants

39 VUS of 49 total submissions

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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.86LOEUF

pLI 0.233

Z-score 1.82

OE 0.27 (0.11–0.86)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.45Z-score

OE missense 0.88 (0.75–1.04)

98 obs / 111.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.27 (0.11–0.86)

0≤0.351.4

Missense OE?0.88 (0.75–1.04)

0≤0.61.4

Synonymous OE?0.83

0≤1.21.6

LoF obs/exp: 2 / 7.3Missense obs/exp: 98 / 111.3Syn Z: 0.85

ClinVar Variant Classifications

49 submitted variants in ClinVar

ClinVar

Classification Summary

VUS39

Likely Benign3

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	39	39
Likely Benign	3	3
Benign	0	0
Total	42	42

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

View in ClinVar →

41 pathogenic / likely-pathogenic (of 60) ClinVar copy-number / structural variants overlap JPT2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →