CPLX1 p.Lys98=
c.294G>A · VCV3778453
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, 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 2 | GERP 0.23, phastCons 1 |
| Overall | ||
| CADD | 13.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,024 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000205%
3/1,460,472 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,512 |
| European (non-Finnish) | 8.48e-05% | 1,179,464 |
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.Lys98=
- Coding
- c.294G>A
- MANE Select
- NM_006651
- Type
- single nucleotide variant
- Location
- chr4:786612 (GRCh38)
- Gene constraint
- LOEUF 0.756 · pLI 0.44 (gnomAD)
- Structure
- AlphaFold pLDDT 72.31 · 2 PDB
- Residue 98
- the 'disordered' region
Similar variants
- 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
- CPLX1 p.Val109Ala 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-lys98 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown