GIT1 p.Pro83=
c.249C>T · rs78783041 · VCV778685
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 5.51%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4 | GERP -3.8 |
| Overall | ||
| CADD | 10.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.51%
African / African-American · 4,138/75,032 alleles
Filtering AF
5.37%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.32%
Overall
0.291%
4,697/1,612,276 alleles · common
exomes 2,350/1,459,954 · genomes 2,347/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.51% | 18 |
| Remaining individualsnot grpmax-eligible | 0.351% | 285 |
| Admixed American | 0.337% | 297 |
| Middle Eastern | 0.264% | 379 |
| European (non-Finnish) | 0.00975% | 10,259 |
| South Asian | 0.00659% | 15,180 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- GIT1
- Protein
- p.Pro83=
- Coding
- c.249C>T
- MANE Select
- NM_014030
- dbSNP
- rs78783041
- Type
- single nucleotide variant
- Location
- chr17:29582975 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.72
- Residue 83
- the arf-gap domain; the 'interaction with gamma-tubulin and localization to the centrosome' region
Similar variants
- GIT1 c.762-205C>T Uncertain significance ★ same type
- GIT1 p.Ala130Thr Uncertain significance ★ ⚠ same type
- GIT1 p.Ala183Gly Uncertain significance ★ same type
- GIT1 p.Ala311Val Uncertain significance ★ ⚠ same type
- GIT1 p.Ala402Thr Uncertain significance ★ ⚠ same type
- GIT1 p.Ala466Val Uncertain significance ★ ⚠ same type
- GIT1 p.Ala488Thr Uncertain significance ★ ⚠ same type
- GIT1 p.Ala488Val Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/git1-p-pro83 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown