CIT p.Ser410=
c.1230G>A · rs765647045 · VCV2973788
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00676%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.149 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.43 | donor gain · deltas |
| Pangolin | Δ0.53 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -3.2 |
| Overall | ||
| CADD | 12.22 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00676%
Admixed American · 4/59,140 alleles
Filtering AF
0.00228%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00191%
Overall
0.0028%
45/1,608,734 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00676% | 14,785 |
| African / African-American | 0.00539% | 18,565 |
| European (non-Finnish) | 0.00297% | 33,656 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,192 |
| Finnishnot grpmax-eligible | 0.00156% | 63,954 |
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.Ser410=
- Coding
- c.1230G>A
- MANE Select
- NM_001206999
- dbSNP
- rs765647045
- Type
- single nucleotide variant
- Location
- chr12:119803271 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.75
- Residue 410
- the agc-kinase c-terminal domain
Similar variants
- CIT p.Ser410Leu Likely benign ★ same residue
- CIT p.Arg1178Ter Pathogenic ★★ same type
- CIT p.Arg220Ter Pathogenic ★★ same type
- CIT c.4168+5G>A Uncertain significance ★★ same type
- CIT p.Ala1144Thr Uncertain significance ★★ ⚠ same type
- CIT p.Ala1466Asp Uncertain significance ★★ ⚠ same type
- CIT p.Ala1527Val Uncertain significance ★★ ⚠ same type
- CIT p.Ala244Val Uncertain significance ★★ ⚠ same type
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-ser410 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown