NIPSNAP2

Chr 7

nipsnap homolog 2

Also known as: GBAS

NCBI Gene: 2631ENSG00000146729UniProt: O75323

This gene encodes a member of the NipSnap family of proteins that may be involved in vesicular transport. The encoded protein is localized to mitochondria and plays a role in oxidative phosphorylation. A pseudogene of this gene is located on the long arm of chromosome 2. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2011]

77
ClinVar variants
12
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— NIPSNAP2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
12 Pathogenic / Likely Pathogenic· 59 VUS of 77 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.
1.12LOEUF
pLI 0.000
Z-score 1.15
OE 0.73 (0.48–1.12)
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.
1.34Z-score
OE missense 0.69 (0.58–0.81)
99 obs / 144.2 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.0.73 (0.48–1.12)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.69 (0.58–0.81)
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.1.15
0≤1.21.6
LoF obs/exp: 15 / 20.6Missense obs/exp: 99 / 144.2Syn Z: -0.85

ClinVar Variant Classifications

77 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic11
Likely Pathogenic1
VUS59
Likely Benign4
Benign2
11
Pathogenic
1
Likely Pathogenic
59
VUS
4
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
11
0
11
Likely Pathogenic
0
0
1
0
1
VUS
0
47
12
0
59
Likely Benign
0
1
3
0
4
Benign
0
0
2
0
2
Total04829077

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

View in ClinVar →

Protein Context — Lollipop Plot

NIPSNAP2 · 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
NIPSNAP1 and NIPSNAP2 Act as "Eat Me" Signals for Mitophagy.
Princely Abudu Y et al.·Dev Cell
2019
Autophagy gene expression in skeletal muscle of older individuals is associated with physical performance, muscle volume and mitochondrial function in the study of muscle, mobility and aging (SOMMA).
Coen PM et al.·Aging Cell
2024
NIPSNAP1 and NIPSNAP2 act as "eat me" signals to allow sustained recruitment of autophagy receptors during mitophagy.
Abudu YP et al.·Autophagy
2019
Characterization of the human NIPSNAP1 gene from 22q12: a member of a novel gene family.
Seroussi E et al.·Gene
1998
Knockdown of GBAS regulates esophageal cancer cell viability and apoptosis.
Peng J et al.·Mol Med Rep
2021
NIP-SNAP-1 and -2 mitochondrial proteins are maintained by heat shock protein 60.
Yamamoto S et al.·Biochem Biophys Res Commun
2017
GBAS, a novel gene encoding a protein with tyrosine phosphorylation sites and a transmembrane domain, is co-amplified with EGFR.
Wang XY et al.·Genomics
1998
Mitochondrial proteins NIP-SNAP-1 and -2 are a target for the immunomodulatory activity of clarithromycin, which involves NF-κB-mediated cytokine production.
Yamamoto S et al.·Biochem Biophys Res Commun
2017
Functional annotation of heart enriched mitochondrial genes GBAS and CHCHD10 through guilt by association.
Martherus RS et al.·Biochem Biophys Res Commun
2010Functional
Sequence variants in four candidate genes (NIPSNAP1, GBAS, CHCHD1 and METT11D1) in patients with combined oxidative phosphorylation system deficiencies.
Smits P et al.·J Inherit Metab Dis
2010Cohort
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