GIT1 c.*3TC[2]
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Conditions
1
GIT1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 9.7 | GERP 0.62, phastCons 1 |
| Overall | ||
| CADD | 14.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,068 alleles
Filtering AF
0.000547%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000432%
Overall
0.000874%
14/1,602,320 alleles · ultra-rare
exomes 13/1,450,196 · genomes 1/152,124 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,068 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,074 |
| European (non-Finnish) | 0.00103% | 97,520 |
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
- Coding
- c.*3TC[2]
- MANE Select
- NM_014030
- dbSNP
- rs2033121800
- Type
- Microsatellite
- Location
- chr17:29574694 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.72
Disease context
GIT1-related disorder
Similar variants
- GIT1 c.1094-1_1096del Pathogenic ★ same condition
- GIT1 p.Ala515fs Pathogenic ★ same condition
- GIT1 c.2010-4G>A Likely benign same condition
- GIT1 p.Ala515= Likely benign same condition
- GIT1 p.Arg717= Likely benign same condition
- GIT1 p.Asp418= Likely benign same condition
- GIT1 p.Gln250= Likely benign same condition
- GIT1 p.Glu221= Likely benign same condition
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-c-star-3tc-2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown