Is PCNA p.Ile11= (c.33C>T) pathogenic?

PCNA p.Ile11= (c.33C>T) is classified Likely benign in PCNA (ClinVar, Single submitter, 1 submitter; last evaluated 2018-04-23). Ultra-rare (popmax 0.0348%, amr).

How common is PCNA p.Ile11= (c.33C>T) in the general population?

PCNA p.Ile11= (c.33C>T) is ultra-rare (popmax 0.0348%, amr) (gnomAD).

PCNA p.Ile11=

c.33C>T · rs141688754 · VCV748972

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0348%, amr)

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 5.8	GERP 1.8, phastCons 1
Overall
CADD	14.02	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0348% Admixed American · 19/54,646 alleles

Filtering AF 0.0227% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0189%

Overall 0.0136% 215/1,580,406 alleles · ultra-rare exomes 198/1,428,066 · genomes 17/152,340 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0348%	2,876
Middle Eastern	0.0208%	4,814
European (non-Finnish)	0.0156%	6,426
Remaining individualsnot grpmax-eligible	0.0131%	7,647
African / African-American	0.00806%	12,412

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: PCNA
Protein: p.Ile11=
Coding: c.33C>T
MANE Select: NM_182649
dbSNP: rs141688754
Type: single nucleotide variant
Location: chr20:5119766 (GRCh38)
Gene constraint: LOEUF 0.42 · pLI 0.99 (gnomAD)
Structure: AlphaFold pLDDT 94.38 · 103 PDB
Residue 11: the 'interaction with nudt15' region; an α-helix

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

Similar variants

PCNA p.Cys148Ser Likely pathogenic ★★ same type
PCNA p.Ser228Ile Uncertain significance ★★ ⚠ same type
PCNA p.Ala242= Benign/Likely benign ★★ same type
PCNA p.Pro234= Benign ★★ same type
PCNA p.Arg53Gln Uncertain significance ★ ⚠ same type
PCNA p.Asn24Ser Uncertain significance ★ ⚠ same type
PCNA p.Gly56Ser Uncertain significance ★ ⚠ same type
PCNA p.Leu182Phe 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/pcna-p-ile11 (accessed [today's date]).

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