CIT p.Ile1356=
c.4068C>A · rs56006347 · VCV3046840
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, afr)
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 -3.5 | GERP -3.6 |
| Overall | ||
| CADD | 0.695 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
African / African-American · 15/74,930 alleles
Filtering AF
0.0123%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00989%
Overall
0.00118%
19/1,613,982 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.02% | 4,995 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| South Asian | 0.0011% | 91,070 |
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.Ile1356=
- Coding
- c.4068C>A
- MANE Select
- NM_001206999
- dbSNP
- rs56006347
- Type
- single nucleotide variant
- Location
- chr12:119718345 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.75
Disease context
CIT-related disorder
Similar variants
- 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.Leu1803= Likely benign same condition
- CIT p.Pro1377= Likely benign same condition
- CIT p.Pro1717= 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-ile1356 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown