PCLO p.Pro4464=
c.13392G>A · rs78925303 · VCV1165450
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.26%, eas)
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 -0.13 | GERP -3.4, phastCons 0.77 |
| Overall | ||
| CADD | 9.245 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.26%
East Asian · 565/44,774 alleles
Filtering AF
1.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.14%
Overall
0.0589%
950/1,612,778 alleles · low-frequency
exomes 848/1,460,700 · genomes 102/152,078 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.26% | 79 |
| Admixed American | 0.192% | 521 |
| Remaining individualsnot grpmax-eligible | 0.0577% | 1,734 |
| South Asian | 0.0264% | 3,794 |
| African / African-American | 0.0254% | 3,943 |
| Middle Eastern | 0.0165% | 6,056 |
| European (non-Finnish) | 0.0161% | 6,206 |
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
- PCLO
- Protein
- p.Pro4464=
- Coding
- c.13392G>A
- MANE Select
- NM_033026
- dbSNP
- rs78925303
- Type
- single nucleotide variant
- Location
- chr7:82908922 (GRCh38)
- Gene constraint
- LOEUF 0.191 · pLI 1.00 (gnomAD)
Similar variants
- PCLO p.Pro4464Leu Benign/Likely benign ★★ same residue
- PCLO p.Ala1410Thr Uncertain significance ★★ ⚠ same type
- PCLO p.Ala2123Val Uncertain significance ★★ ⚠ same type
- PCLO p.Ala2259Gly Uncertain significance ★★ ⚠ same type
- PCLO p.Ala3066Ser Uncertain significance ★★ ⚠ same type
- PCLO p.Ala3613Ser Uncertain significance ★★ ⚠ same type
- PCLO p.Ala3662Thr Uncertain significance ★★ ⚠ same type
- PCLO p.Ala3695Val 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/pclo-p-pro4464 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown