CPLANE1 p.Val112=
c.336C>T · rs571875820 · VCV261669
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0101%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.65 · evaluated, not missing |
|---|---|---|
| Pangolin | Δ0.22 | loss · gain 0.02 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.82 | GERP -1.8, phastCons 0.97 |
| Overall | ||
| CADD | 13.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0101%
European (non-Finnish) · 110/1,088,480 alleles
Filtering AF
0.00857%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00797%
Overall
0.00872%
125/1,434,258 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0101% | 9,895 |
| Remaining individualsnot grpmax-eligible | 0.00915% | 10,930 |
| African / African-American | 0.00731% | 13,672 |
| Admixed American | 0.00575% | 17,383 |
| East Asian | 0.0027% | 37,020 |
| Finnishnot grpmax-eligible | 0.00177% | 56,616 |
| South Asian | 0.00159% | 63,010 |
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.Val112=
- Coding
- c.336C>T
- MANE Select
- NM_001384732
- dbSNP
- rs571875820
- Type
- single nucleotide variant
- Location
- chr5:37245480 (GRCh38)
- Gene constraint
- LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Similar variants
- CPLANE1 p.Val112Phe Uncertain significance ★ ⚠ 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
- CPLANE1 c.2920+1G>A Likely pathogenic ★★ same type
- CPLANE1 c.3290-2A>G 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/cplane1-p-val112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown