PCLO p.Pro401=
c.1203A>G · rs371251879 · VCV1551420
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.115%, mid)
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 -0.45 | GERP 0.41 |
| Overall | ||
| CADD | 8.505 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.115%
Middle Eastern · 7/6,062 alleles
Filtering AF
0.0914%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0843%
Overall
0.00694%
112/1,613,872 alleles · rare
exomes 62/1,461,674 · genomes 50/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.115% | 866 |
| African / African-American | 0.111% | 904 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,810 |
| Admixed American | 0.01% | 10,001 |
| European (non-Finnish) | 0.000678% | 147,484 |
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.Pro401=
- Coding
- c.1203A>G
- MANE Select
- NM_033026
- dbSNP
- rs371251879
- Type
- single nucleotide variant
- Location
- chr7:83155438 (GRCh38)
- Gene constraint
- LOEUF 0.191 · pLI 1.00 (gnomAD)
- Residue 401
- the 'disordered' region; the '10 x 10 aa tandem approximate repeats of p-a-k-p-q-p-q-q-p-x' region
Similar variants
- 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
- PCLO p.Ala3811Gly 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-pro401 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown