CIT p.Tyr6=
c.18T>C · rs755628356 · VCV3047701
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00892%, eas)
Conditions
1
CIT-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 6 | GERP 0.8, phastCons 1 |
| Overall | ||
| CADD | 10.73 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00892%
East Asian · 4/44,838 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00195%
Overall
0.00118%
19/1,613,472 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00892% | 11,210 |
| South Asian | 0.00659% | 15,170 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,470 |
| European (non-Finnish) | 0.000678% | 147,460 |
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
- CIT
- Protein
- p.Tyr6=
- Coding
- c.18T>C
- MANE Select
- NM_001206999
- dbSNP
- rs755628356
- Type
- single nucleotide variant
- Location
- chr12:119876151 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.75
Disease context
CIT-related disorder
Similar variants
- CIT p.Tyr6His Uncertain significance ★ ⚠ same residue
- CIT p.Gln64Ter Likely pathogenic ★ same condition
- CIT c.2532-9C>T Likely benign same condition
- CIT c.3486+7G>A Likely benign same condition
- CIT c.6187-4C>T Likely benign same condition
- CIT p.Asn1972= Likely benign same condition
- CIT p.Ile1356= Likely benign same condition
- CIT p.Leu1803= 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/cit-p-tyr6 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown