CPLX1 p.Arg59=
c.177C>T · rs541047416 · VCV2076054
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0353%, sas)
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 -5 | GERP -3 |
| Overall | ||
| CADD | 6.949 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0353%
South Asian · 32/90,638 alleles
Filtering AF
0.0257%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0223%
Overall
0.00243%
39/1,607,596 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0353% | 2,832 |
| Admixed American | 0.0101% | 9,935 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,226 |
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
- CPLX1
- Protein
- p.Arg59=
- Coding
- c.177C>T
- MANE Select
- NM_006651
- dbSNP
- rs541047416
- Type
- single nucleotide variant
- Location
- chr4:792463 (GRCh38)
- Gene constraint
- LOEUF 0.756 · pLI 0.44 (gnomAD)
- Structure
- AlphaFold pLDDT 72.31 · 2 PDB
- Residue 59
- the 'disordered' region; the 'interaction with the snare complex' region; an α-helix
Similar variants
- CPLX1 p.Arg59Cys Uncertain significance ★ ⚠ same residue
- CPLX1 p.Cys105Ter Pathogenic/Likely pathogenic ★★ same type
- CPLX1 p.Glu108Ter Likely pathogenic ★★ same type
- CPLX1 p.Asp113Glu Uncertain significance ★★ ⚠ same type
- CPLX1 p.Asp29Ala Uncertain significance ★★ ⚠ same type
- CPLX1 p.Gly104Asp Uncertain significance ★★ ⚠ same type
- CPLX1 p.Lys75Glu Uncertain significance ★★ ⚠ same type
- CPLX1 p.Tyr70Ter 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/cplx1-p-arg59 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown