Is PCNA p.Thr51= (c.153C>G) pathogenic?

PCNA p.Thr51= (c.153C>G) is classified Likely benign in PCNA (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-01). Ultra-rare (popmax 0.0719%, afr); Associated with PCNA-related disorder.

What condition is associated with PCNA p.Thr51= (c.153C>G)?

PCNA p.Thr51= (c.153C>G) is associated with PCNA-related disorder (ClinVar).

How common is PCNA p.Thr51= (c.153C>G) in the general population?

PCNA p.Thr51= (c.153C>G) is ultra-rare (popmax 0.0719%, afr) (gnomAD).

PCNA p.Thr51=

c.153C>G · VCV3353150

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0719%, afr)

Conditions

PCNA-related disorder

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 -0.27	GERP -3.8, phastCons 0.025
Overall
CADD	7.142	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0719% African / African-American · 54/75,062 alleles

Filtering AF 0.0566% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0511%

Overall 0.00409% 66/1,613,736 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0719%	1,390
Remaining individualsnot grpmax-eligible	0.0112%	8,924
Admixed American	0.005%	19,995
European (non-Finnish)	0.00017%	589,953

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.Thr51=
Coding: c.153C>G
MANE Select: NM_182649
Type: single nucleotide variant
Location: chr20:5119646 (GRCh38)
Gene constraint: LOEUF 0.42 · pLI 0.99 (gnomAD)
Structure: AlphaFold pLDDT 94.38 · 103 PDB
Residue 51: the 'interaction with nudt15' region; a β-strand

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

Disease context

PCNA-related disorder

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-thr51 (accessed [today's date]).

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