GIT1 p.Ala515fs
c.1541dup · VCV4281612
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
GIT1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 14 of 20 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -6.9 | GERP -3.5 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- GIT1
- Protein
- p.Ala515fs
- Coding
- c.1541dup
- MANE Select
- NM_014030
- Type
- Duplication
- Location
- chr17:29576289 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.72
- Residue 515
- the 'interaction with nck2 and grin3a' region; the 'required for localization at synapses' region; the 'interaction with ikbkg' region
Disease context
GIT1-related disorder
Similar variants
- GIT1 p.Ala515= Likely benign same residue
- GIT1 p.Ala515Ser Uncertain significance ★ ⚠ same residue
- GIT1 c.1094-1_1096del Pathogenic ★ same condition
- GIT1 c.2010-4G>A Likely benign same condition
- GIT1 c.*3TC[2] 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
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-ala515fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown