Is GIT1 p.Ala402Thr (c.1204G>A) pathogenic?

GIT1 p.Ala402Thr (c.1204G>A) is classified Uncertain significance in GIT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-29). AlphaMissense: likely benign (0.0614); Ultra-rare (popmax 0.0194%, mid); Associated with Inborn genetic diseases.

What condition is associated with GIT1 p.Ala402Thr (c.1204G>A)?

GIT1 p.Ala402Thr (c.1204G>A) is associated with Inborn genetic diseases (ClinVar).

How common is GIT1 p.Ala402Thr (c.1204G>A) in the general population?

GIT1 p.Ala402Thr (c.1204G>A) is ultra-rare (popmax 0.0194%, mid) (gnomAD).

What do computational predictors say about GIT1 p.Ala402Thr (c.1204G>A)?

AlphaMissense predicts likely benign (score 0.0614) — an in-silico prediction, not a clinical call.

GIT1 p.Ala402Thr

c.1204G>A · VCV3854035

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0614 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0194%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0614	likely benign
REVEL	0.114	moderately benign-leaning
SaProt	LLR -6.49	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.053	GERP -3.8
Regional constraint	o/e 0.89	unconstrained · MANE · 1,519 bp · p 0.045 · regional, not allelic
Overall
CADD	12.76	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0194% Middle Eastern · 1/5,160 alleles

Filtering AF 0.00533% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00399%

Overall 0.000698% 11/1,575,270 alleles · ultra-rare exomes 11/1,422,962 · genomes 0/152,308 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0194%	5,160
South Asian	0.0103%	9,715
European (non-Finnish)	8.6e-05%	1,162,156

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.Ala402Thr
Coding: c.1204G>A
MANE Select: NM_014030
Type: single nucleotide variant
Location: chr17:29576886 (GRCh38)
Gene constraint: LOEUF 0.257 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 74.72
Residue 402: the 'disordered' region; the 'interaction with nck2 and grin3a' region; the 'required for localization at synapses' region; the 'interaction with ptk2/fak1' region

Full GIT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GIT1 c.762-205C>T Uncertain significance ★ same condition
GIT1 p.Ala130Thr Uncertain significance ★ ⚠ same condition
GIT1 p.Ala183Gly Uncertain significance ★ same condition
GIT1 p.Ala311Val Uncertain significance ★ ⚠ same condition
GIT1 p.Ala466Val Uncertain significance ★ ⚠ same condition
GIT1 p.Ala488Thr Uncertain significance ★ ⚠ same condition
GIT1 p.Ala488Val Uncertain significance ★ ⚠ same condition
GIT1 p.Ala515Ser Uncertain significance ★ ⚠ 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-ala402thr (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown