GIT1 p.Thr400=
c.1200C>T · rs141462052 · VCV3040526
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.88%, afr)
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 · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.2 | GERP -3.8 |
| Overall | ||
| CADD | 0.999 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.88%
African / African-American · 1,398/74,440 alleles
Filtering AF
1.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.76%
Overall
0.0993%
1,565/1,575,784 alleles · low-frequency
exomes 771/1,423,480 · genomes 794/152,304 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.88% | 53 |
| Remaining individualsnot grpmax-eligible | 0.0833% | 1,200 |
| Admixed American | 0.0831% | 1,203 |
| European (non-Finnish) | 0.00602% | 16,606 |
| South Asian | 0.00228% | 43,783 |
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.Thr400=
- Coding
- c.1200C>T
- MANE Select
- NM_014030
- dbSNP
- rs141462052
- Type
- single nucleotide variant
- Location
- chr17:29576890 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.72
- Residue 400
- the 'disordered' region; the 'interaction with nck2 and grin3a' region; the 'required for localization at synapses' region; the 'interaction with ptk2/fak1' region
Disease context
GIT1-related disorder
Similar variants
- 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
- GIT1 p.Glu622= Likely benign same condition
- GIT1 p.His50= 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-p-thr400 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown