CLTA p.Arg129=
c.387G>A · rs149517035 · VCV788300
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.78%, amr)
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 3.1 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 12.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.78%
Admixed American · 1,068/60,000 alleles
Filtering AF
1.69%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.66%
Overall
0.0693%
1,119/1,614,058 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 1.78% | 56 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,155 |
| African / African-American | 0.0173% | 5,771 |
| European (non-Finnish) | 0.000763% | 131,108 |
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
- CLTA
- Protein
- p.Arg129=
- Coding
- c.387G>A
- MANE Select
- NM_001833
- dbSNP
- rs149517035
- Type
- single nucleotide variant
- Location
- chr9:36204081 (GRCh38)
- Gene constraint
- LOEUF 0.546 · pLI 0.94 (gnomAD)
- Structure
- AlphaFold pLDDT 72.20 · 1 PDB
- Residue 129
- the 'involved in binding clathrin heavy chain' region
Similar variants
- CLTA p.Arg129Gln Uncertain significance ★ ⚠ same residue
- CLTA p.Arg129Trp Uncertain significance ★ same residue
- CLTA c.256-6G>A Benign ★★ same type
- CLTA c.486-2284G>A Uncertain significance ★ ⚠ same type
- CLTA c.486-971A>G Uncertain significance ★ ⚠ same type
- CLTA p.Ala11Gly Uncertain significance ★ ⚠ same type
- CLTA p.Ala133Thr Uncertain significance ★ ⚠ same type
- CLTA p.Ala18Thr 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/clta-p-arg129 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown