Is PDCD4 p.Ser389= (c.1167C>T) pathogenic?

PDCD4 p.Ser389= (c.1167C>T) is classified Benign in PDCD4 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-05-21). Rare (popmax 0.378%, nfe).

How common is PDCD4 p.Ser389= (c.1167C>T) in the general population?

PDCD4 p.Ser389= (c.1167C>T) is rare (popmax 0.378%, nfe) (gnomAD).

PDCD4 p.Ser389=

c.1167C>T · rs41292602 · VCV710229

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.378%, nfe)

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 -0.51	GERP -3.8, phastCons 0.041
Overall
CADD	3.942	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.378% European (non-Finnish) · 4,304/1,138,472 alleles

Filtering AF 0.369% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.365%

Overall 0.344% 5,394/1,566,110 alleles · rare exomes 4,930/1,414,220 · genomes 464/151,890 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	1.75%	57
Amishnot grpmax-eligible	0.658%	152
Remaining individualsnot grpmax-eligible	0.381%	263
European (non-Finnish)grpmax	0.378%	265
Middle Eastern	0.286%	349
Admixed American	0.182%	548
Finnishnot grpmax-eligible	0.144%	694
South Asian	0.0833%	1,200
African / African-American	0.0676%	1,480

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: PDCD4
Protein: p.Ser389=
Coding: c.1167C>T
MANE Select: NM_014456
dbSNP: rs41292602
Type: single nucleotide variant
Location: chr10:110894480 (GRCh38)
Gene constraint: LOEUF 1.671 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.03 · 11 PDB
Residue 389: the mi 2 domain; an α-helix

Full PDCD4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PDCD4 p.Ala118Val Uncertain significance ★ ⚠ same type
PDCD4 p.Ala84Thr Uncertain significance ★ ⚠ same type
PDCD4 p.Arg310Cys Uncertain significance ★ ⚠ same type
PDCD4 p.Arg428Trp Uncertain significance ★ ⚠ same type
PDCD4 p.Arg61Thr Uncertain significance ★ ⚠ same type
PDCD4 p.Arg69Trp Uncertain significance ★ ⚠ same type
PDCD4 p.Asn410Ser Uncertain significance ★ ⚠ same type
PDCD4 p.Asp144His 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/pdcd4-p-ser389 (accessed [today's date]).

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