CIC p.Pro1990=
c.5970G>A · rs768415690 · VCV3052853
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
CIC-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 0.7 | GERP -3.4, phastCons 1 |
| Overall | ||
| CADD | 8.713 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00892%
East Asian · 4/44,846 alleles
Filtering AF
0.00555%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00514%
Overall
0.00546%
88/1,611,124 alleles · very rare
exomes 84/1,459,012 · genomes 4/152,112 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00892% | 11,212 |
| European (non-Finnish) | 0.00678% | 14,743 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,586 |
| African / African-American | 0.00267% | 37,442 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,236 |
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.Pro1990=
- Coding
- c.5970G>A
- MANE Select
- NM_001386298
- dbSNP
- rs768415690
- Type
- single nucleotide variant
- Location
- chr19:42292633 (GRCh38)
- Structure
- AlphaFold pLDDT 75.09
Disease context
CIC-related disorder
Similar variants
- CIC p.Asn1136Ser Likely pathogenic ★★ same condition
- SLC25A1 p.Ala274Val Pathogenic/Likely pathogenic ★★ same condition
- SLC25A1 p.Glu174Ter Pathogenic/Likely pathogenic ★★ same condition
- CIC p.Arg2114Trp Uncertain significance ★★ ⚠ same condition
- CIC p.Arg800His Uncertain significance ★★ same condition
- CIC p.Gly17Val Uncertain significance ★★ same condition
- CIC p.Val989Ala Uncertain significance ★★ same condition
- CIC p.Arg800Cys Likely pathogenic ★ 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/cic-p-pro1990 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown