Is PCLO p.Pro511= (c.1533T>A) pathogenic?

PCLO p.Pro511= (c.1533T>A) is classified Likely benign in PCLO (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-19). Absent from gnomAD v4.1.

How common is PCLO p.Pro511= (c.1533T>A) in the general population?

PCLO p.Pro511= (c.1533T>A) is absent from gnomAD v4.1 (gnomAD).

PCLO p.Pro511=

c.1533T>A · rs2116686634 · VCV1664482

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,439,632)

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 -0.054	GERP -2.6
Overall
CADD	1.874	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,439,632). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PCLO
Protein: p.Pro511=
Coding: c.1533T>A
MANE Select: NM_033026
dbSNP: rs2116686634
Type: single nucleotide variant
Location: chr7:83155108 (GRCh38)
Gene constraint: LOEUF 0.191 · pLI 1.00 (gnomAD)
Residue 511: the 'disordered' region; the '10 x 10 aa tandem approximate repeats of p-a-k-p-q-p-q-q-p-x' region

Full PCLO gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PCLO p.Pro511Arg Uncertain significance ★ ⚠ same residue
PCLO p.Pro511Ser Likely benign ★ same residue
PCLO p.Pro511_Pro530del Uncertain significance ★ 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

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-pro511 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown