CTTN p.Tyr489=
c.1467C>T · rs138763797 · VCV711554
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.652%, 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 -4.1 | GERP -4.5 |
| Overall | ||
| CADD | 0.576 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.652%
African / African-American · 489/74,992 alleles
Filtering AF
0.604%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.585%
Overall
0.0364%
587/1,613,382 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.652% | 153 |
| Admixed American | 0.055% | 1,819 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,155 |
| Middle Eastern | 0.033% | 3,031 |
| South Asian | 0.00769% | 13,008 |
| East Asian | 0.00223% | 44,852 |
| European (non-Finnish) | 0.0022% | 45,362 |
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
- CTTN
- Protein
- p.Tyr489=
- Coding
- c.1467C>T
- MANE Select
- NM_005231
- dbSNP
- rs138763797
- Type
- single nucleotide variant
- Location
- chr11:70433669 (GRCh38)
- Gene constraint
- LOEUF 0.48 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 63.11 · 5 PDB
- Residue 489
- a modified residue (phosphotyrosine; by src)
Similar variants
- CTTN p.Val312= Benign ★★ same type
- CTTN p.Val340Gly Likely benign ★★ same type
- CTTN c.*1144C>G Uncertain significance ★ same type
- CTTN c.*1145C>T Uncertain significance ★ same type
- CTTN c.*1154G>A Uncertain significance ★ same type
- CTTN c.*1164C>T Uncertain significance ★ same type
- CTTN c.*1167C>T Uncertain significance ★ same type
- CTTN c.*1173G>A 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/cttn-p-tyr489 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown