Is PDCD1 p.Pro160= (c.480C>G) pathogenic?

PDCD1 p.Pro160= (c.480C>G) is classified Likely benign in PDCD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-11-04). Ultra-rare (popmax 0.0135%, nfe); Associated with PDCD1-related disorder.

What condition is associated with PDCD1 p.Pro160= (c.480C>G)?

PDCD1 p.Pro160= (c.480C>G) is associated with PDCD1-related disorder (ClinVar).

How common is PDCD1 p.Pro160= (c.480C>G) in the general population?

PDCD1 p.Pro160= (c.480C>G) is ultra-rare (popmax 0.0135%, nfe) (gnomAD).

PDCD1 p.Pro160=

c.480C>G · rs370660750 · VCV3045064

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0135%, nfe)

Conditions

PDCD1-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 0.64	GERP -1.2, phastCons 0.14
Overall
CADD	5.061	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0135% European (non-Finnish) · 159/1,178,772 alleles

Filtering AF 0.0117% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0111%

Overall 0.0106% 170/1,610,840 alleles · ultra-rare exomes 154/1,458,736 · genomes 16/152,104 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0135%	7,414
Remaining individualsnot grpmax-eligible	0.00963%	10,384
Admixed American	0.00501%	19,956
African / African-American	0.00267%	37,425

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: PDCD1
Protein: p.Pro160=
Coding: c.480C>G
MANE Select: NM_005018
dbSNP: rs370660750
Type: single nucleotide variant
Location: chr2:241852310 (GRCh38)
Gene constraint: LOEUF 0.891 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 74.53 · 38 PDB

Full PDCD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

PDCD1-related disorder

Similar variants

PDCD1 c.436+10C>T Likely benign same condition
PDCD1 c.437-8C>T Likely benign same condition
PDCD1 c.627+189G>C Benign same condition
PDCD1 c.437-115G>A Benign ★★ same type
PDCD1 c.593-56C>G Benign ★★ same type
PDCD1 c.627+189G>A Benign ★★ same type
PDCD1 c.628-110A>G Benign ★★ same type
PDCD1 c.76+126G>C Benign ★★ 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/pdcd1-p-pro160 (accessed [today's date]).

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