GIT1 p.His50=
c.150C>T · rs147244911 · VCV3045426
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.231%, 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 · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.6 | GERP 0.94, phastCons 1 |
| Overall | ||
| CADD | 11.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.231%
Middle Eastern · 14/6,062 alleles
Filtering AF
0.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.112%
Overall
0.0595%
959/1,612,588 alleles · rare
exomes 882/1,460,282 · genomes 77/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.231% | 433 |
| European (non-Finnish) | 0.0678% | 1,475 |
| Admixed American | 0.0667% | 1,500 |
| Finnishnot grpmax-eligible | 0.0527% | 1,896 |
| Remaining individualsnot grpmax-eligible | 0.0512% | 1,952 |
| South Asian | 0.034% | 2,938 |
| African / African-American | 0.00933% | 10,719 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,799 |
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.His50=
- Coding
- c.150C>T
- MANE Select
- NM_014030
- dbSNP
- rs147244911
- Type
- single nucleotide variant
- Location
- chr17:29583519 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.72
- Residue 50
- the arf-gap domain; the 'interaction with gamma-tubulin and localization to the centrosome' 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.Leu516= 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-his50 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown