NIBAN2

Chr 9

niban apoptosis regulator 2

Also known as: C9orf88, FAM129B, MEG-3, MINERVA, OC58, bA356B19.6

NCBI Gene: 64855ENSG00000136830UniProt: Q96TA1OMIM: 614045

NIBAN2 encodes a transcription coactivator that suppresses apoptosis and is involved in regulating nucleotide metabolism and gonadotropin secretion. Mutations cause autosomal recessive neurodevelopmental disorder with early infantile epileptic encephalopathy, developmental delay, and intellectual disability. The gene is highly constrained against loss-of-function variants, indicating that biallelic mutations are likely required for disease manifestation.

OMIMResearchSummary from RefSeq, UniProt
GOFmechanismLOEUF 0.45
Clinical Summary— NIBAN2
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.28) despite low pLI — interpret in context.
📋
ClinVar Variants
39 unique Pathogenic / Likely Pathogenic· 149 VUS of 215 total submissions
💊
Clinical Trials
2 active or recruiting trials — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.45LOEUF
pLI 0.017
Z-score 4.44
OE 0.28 (0.17–0.45)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.42Z-score
OE missense 0.95 (0.87–1.02)
445 obs / 470.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.28 (0.17–0.45)
0≤0.351.4
Missense OE0.95 (0.87–1.02)
0≤0.61.4
Synonymous OE0.94
0≤1.21.6
LoF obs/exp: 12 / 43.6Missense obs/exp: 445 / 470.6Syn Z: 0.69
DN
0.5280th %ile
GOF
0.7126th %ile
LOF
0.4038th %ile

The highest-scoring mechanism for this gene is gain-of-function.

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

215 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic38
Likely Pathogenic1
VUS149
Likely Benign8
38
Pathogenic
1
Likely Pathogenic
149
VUS
8
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
38
0
38
Likely Pathogenic
0
0
1
0
1
VUS
0
145
4
0
149
Likely Benign
0
5
1
2
8
Benign
0
0
0
0
0
Total0150442196

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

View in ClinVar →

Protein Context — Lollipop Plot

NIBAN2 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 2 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients