CGN p.Ile60=
c.180C>T · rs142876758 · VCV711289
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.64%, afr)
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 -7.9 | GERP -4.4 |
| Overall | ||
| CADD | 1.219 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.64%
African / African-American · 1,233/75,026 alleles
Filtering AF
1.57%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.54%
Overall
0.207%
3,340/1,614,132 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.64% | 61 |
| Finnishnot grpmax-eligible | 0.504% | 198 |
| Remaining individualsnot grpmax-eligible | 0.29% | 345 |
| Middle Eastern | 0.248% | 404 |
| Ashkenazi Jewishnot grpmax-eligible | 0.22% | 455 |
| Admixed American | 0.193% | 517 |
| European (non-Finnish) | 0.116% | 866 |
| South Asian | 0.0439% | 2,277 |
| East Asian | 0.00891% | 11,220 |
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
- CGN
- Protein
- p.Ile60=
- Coding
- c.180C>T
- MANE Select
- NM_020770
- dbSNP
- rs142876758
- Type
- single nucleotide variant
- Location
- chr1:151518699 (GRCh38)
- Gene constraint
- LOEUF 0.88 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.44
- Residue 60
- the 'head' region; the 'interaction with tjp1/zo1' region
Similar variants
- CGN p.Ala357= Benign/Likely benign ★★ same type
- CGN p.Arg11Trp Likely benign ★★ same type
- CGN p.Arg227Trp Likely benign ★★ same type
- CGN p.Arg547Lys Benign ★★ same type
- CGN p.Arg973Gln Benign ★★ same type
- CGN p.Glu771Lys Benign/Likely benign ★★ same type
- CGN p.Ala1035Thr Uncertain significance ★ same type
- CGN p.Ala142Val 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/cgn-p-ile60 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown