GIT1 p.Pro569=
c.1707C>T · VCV4934410
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.20 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.89 | GERP -3, phastCons 1 |
| Overall | ||
| CADD | 8.863 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,778 alleles
Overall
0.000124%
2/1,612,016 alleles · very rare
exomes 2/1,459,728 · genomes 0/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,778 |
| Finnishnot grpmax-eligible | 0.00157% | 63,740 |
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.Pro569=
- Coding
- c.1707C>T
- MANE Select
- NM_014030
- Type
- single nucleotide variant
- Location
- chr17:29575857 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.72
- Residue 569
- the 'interaction with nck2 and grin3a' region; the 'required for localization at synapses' region; the 'interaction with ikbkg' region
Similar variants
- GIT1 p.Pro83= Benign ★★ same type
- 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
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-pro569 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown