GIT1 p.Ser370=
c.1110T>G · rs144787773 · VCV717463
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0498%, nfe)
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 0.27 | GERP -3.7 |
| Overall | ||
| CADD | 6.464 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0498%
European (non-Finnish) · 588/1,179,656 alleles
Filtering AF
0.0464%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0451%
Overall
0.0387%
621/1,602,804 alleles · ultra-rare
exomes 579/1,450,644 · genomes 42/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0498% | 2,006 |
| Remaining individualsnot grpmax-eligible | 0.0385% | 2,600 |
| African / African-American | 0.00801% | 12,480 |
| Admixed American | 0.00334% | 29,926 |
| Finnishnot grpmax-eligible | 0.00187% | 53,506 |
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.Ser370=
- Coding
- c.1110T>G
- MANE Select
- NM_014030
- dbSNP
- rs144787773
- Type
- single nucleotide variant
- Location
- chr17:29576980 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.72
- Residue 370
- the 'disordered' region; the 'interaction with nck2 and grin3a' region; the 'required for localization at synapses' region; a modified residue (phosphoserine); the 'interaction with ptk2/fak1' 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-ser370 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown