CTAGE1 p.Pro496=
c.1488T>C · rs112281251 · VCV741513
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.191%, 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 8.7 | GERP -3.7, phastCons 1 |
| Overall | ||
| CADD | 1.453 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.191%
African / African-American · 143/75,056 alleles
Filtering AF
0.165%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.155%
Overall
0.0104%
168/1,613,996 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.191% | 525 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,676 |
| Middle Eastern | 0.0165% | 6,056 |
| Admixed American | 0.005% | 20,008 |
| South Asian | 0.0011% | 91,072 |
| European (non-Finnish) | 0.000254% | 393,287 |
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
- CTAGE1
- Protein
- p.Pro496=
- Coding
- c.1488T>C
- MANE Select
- NM_172241
- dbSNP
- rs112281251
- Type
- single nucleotide variant
- Location
- chr18:22416324 (GRCh38)
- Structure
- AlphaFold pLDDT 70.45
Similar variants
- CTAGE1 p.Ala169= Benign ★★ same type
- CTAGE1 p.Ile682Met Benign ★★ same type
- CTAGE1 p.Pro686Thr Benign ★★ ⚠ same type
- CTAGE1 p.Val696Met Benign ★★ same type
- CTAGE1 p.Ala181Val Uncertain significance ★ ⚠ same type
- CTAGE1 p.Ala19Thr Uncertain significance ★ ⚠ same type
- CTAGE1 p.Ala282Asp Uncertain significance ★ ⚠ same type
- CTAGE1 p.Ala332Thr 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/ctage1-p-pro496 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown