CPLANE1 p.Ser1127=
c.3381G>A · rs566190241 · VCV1059994
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.011%, 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 -6.2 | GERP -3.5 |
| Overall | ||
| CADD | 3.937 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.011%
South Asian · 10/91,080 alleles
Filtering AF
0.00594%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00453%
Overall
0.00137%
20/1,461,766 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.011% | 9,108 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,625 |
| European (non-Finnish) | 0.000509% | 196,655 |
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
- CPLANE1
- Protein
- p.Ser1127=
- Coding
- c.3381G>A
- MANE Select
- NM_001384732
- dbSNP
- rs566190241
- Type
- single nucleotide variant
- Location
- chr5:37201717 (GRCh38)
- Gene constraint
- LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 1127
- a UniProt-annotated variant site (in ofd6)
Similar variants
- CPLANE1 p.Ser1127Leu Pathogenic/Likely pathogenic ★★ ⚠ same residue
- CPLANE1 p.Ser1127Ala Uncertain significance ★★ ⚠ same residue
- CPLANE1 p.Ser1127Ter Pathogenic ★ same residue
- CPLANE1 c.1372-2A>G Pathogenic/Likely pathogenic ★★ same type
- CPLANE1 c.2291+1G>A Likely pathogenic ★★ same type
- CPLANE1 c.2291+2T>C Pathogenic/Likely pathogenic ★★ same type
- CPLANE1 c.2292-1G>A Likely pathogenic ★★ same type
- CPLANE1 c.2500+1G>A 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/cplane1-p-ser1127 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown