TTLL5 p.Arg409=
c.1227G>T · rs1191504919 · VCV1103869
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
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 2.2 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 7.35 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,179,988 alleles
Overall
6.2e-05%
1/1,614,182 alleles · very rare
exomes 1/1,461,834 · genomes 0/152,348 · joint denominator
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
- TTLL5
- Protein
- p.Arg409=
- Coding
- c.1227G>T
- MANE Select
- NM_015072
- dbSNP
- rs1191504919
- Type
- single nucleotide variant
- Location
- chr14:75735235 (GRCh38)
- Gene constraint
- LOEUF 0.888 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.56 · 1 PDB
- Residue 409
- the 'c-mtbd region' region
Similar variants
- TTLL5 p.Arg409Trp Uncertain significance ★★ ⚠ same residue
- TTLL5 p.Arg409Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- TTLL5 c.1488-1G>T Likely pathogenic ★★ same type
- TTLL5 c.182-1G>T Likely pathogenic ★★ same type
- TTLL5 c.2388-2A>G Likely pathogenic ★★ same type
- TTLL5 c.3172-2A>G Likely pathogenic ★★ same type
- TTLL5 c.741-1G>A Pathogenic/Likely pathogenic ★★ same type
- TTLL5 p.Arg1170Ter 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/ttll5-p-arg409 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown