CIC p.Lys2239=
c.6717G>A · rs147920519 · VCV742957
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.158%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6.7 | GERP 0.41, phastCons 1 |
| Overall | ||
| CADD | 14.97 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.158%
South Asian · 144/91,046 alleles
Filtering AF
0.137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.129%
Overall
0.0571%
921/1,612,754 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.158% | 632 |
| Middle Eastern | 0.0826% | 1,211 |
| Admixed American | 0.0716% | 1,396 |
| European (non-Finnish) | 0.0585% | 1,710 |
| Remaining individualsnot grpmax-eligible | 0.0512% | 1,952 |
| African / African-American | 0.00799% | 12,513 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,586 |
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
- CIC
- Protein
- p.Lys2239=
- Coding
- c.6717G>A
- MANE Select
- NM_005984 · reported on NM_001386298
- dbSNP
- rs147920519
- Type
- single nucleotide variant
- Location
- chr19:42293786 (GRCh38)
- Structure
- AlphaFold pLDDT 75.09
Similar variants
- CIC c.3179+1G>A Likely pathogenic ★★ same type
- CIC c.3179+1G>T Pathogenic ★★ same type
- CIC c.5903-2A>G Likely pathogenic ★★ same type
- CIC p.Asn1136Ser Likely pathogenic ★★ same type
- CIC p.Gln1134Ter Pathogenic ★★ same type
- CIC p.Gln1799Ter Likely pathogenic ★★ same type
- SLC25A1 c.821+1G>A Pathogenic ★★ same type
- SLC25A1 p.Ala274Val Pathogenic/Likely pathogenic ★★ 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/cic-p-lys2239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown