TUBGCP2

Chr 10AR

tubulin gamma complex component 2

Also known as: ALP4, GCP-2, GCP2, Grip103, PAMDDFS, SPBC97, SPC97, Spc97p

NCBI Gene: 10844ENSG00000130640UniProt: Q9BSJ2OMIM: 617817

The TUBGCP2 protein is a component of the gamma-tubulin ring complex that mediates microtubule nucleation, which is critical for centrosome duplication and spindle formation during cell division. Biallelic mutations cause autosomal recessive pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures. This gene shows low constraint against loss-of-function variants (LOEUF 0.68), and the associated disorder affects brain development and neuronal migration.

OMIMResearchSummary from RefSeq, OMIM, UniProt
MultiplemechanismARLOEUF 0.681 OMIM phenotype
Clinical Summary— TUBGCP2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
11 unique Pathogenic / Likely Pathogenic· 124 VUS of 200 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.68LOEUF
pLI 0.000
Z-score 3.21
OE 0.47 (0.33–0.68)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.24Z-score
OE missense 0.85 (0.79–0.92)
491 obs / 574.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.47 (0.33–0.68)
0≤0.351.4
Missense OE0.85 (0.79–0.92)
0≤0.61.4
Synonymous OE1.07
0≤1.21.6
LoF obs/exp: 20 / 42.6Missense obs/exp: 491 / 574.7Syn Z: -0.94
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
strongTUBGCP2-related microcephaly and lissencephaly spectrum disordersOTHERAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.6357th %ile
GOF
0.6638th %ile
LOF
0.3065th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

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

ClinVar Variant Classifications

200 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic11
VUS124
Likely Benign29
Conflicting1
11
Pathogenic
124
VUS
29
Likely Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
11
0
11
Likely Pathogenic
0
0
0
0
0
VUS
1
123
0
0
124
Likely Benign
0
8
5
16
29
Benign
0
0
0
0
0
Conflicting
—1
Total11311616165

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

View in ClinVar →

Protein Context — Lollipop Plot

TUBGCP2 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
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 5 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