Is PTCD3 p.Trp9Arg (c.25T>C) pathogenic?

PTCD3 p.Trp9Arg (c.25T>C) is classified Uncertain significance in PTCD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-22). AlphaMissense: likely benign (0.2546); Very rare (popmax 0.0022%, sas); Associated with Inborn genetic diseases.

What condition is associated with PTCD3 p.Trp9Arg (c.25T>C)?

PTCD3 p.Trp9Arg (c.25T>C) is associated with Inborn genetic diseases (ClinVar).

How common is PTCD3 p.Trp9Arg (c.25T>C) in the general population?

PTCD3 p.Trp9Arg (c.25T>C) is very rare (popmax 0.0022%, sas) (gnomAD).

What do computational predictors say about PTCD3 p.Trp9Arg (c.25T>C)?

AlphaMissense predicts likely benign (score 0.2546) — an in-silico prediction, not a clinical call.

PTCD3 p.Trp9Arg

c.25T>C · VCV3784561

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2546 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2546	likely benign
REVEL	0.063	moderately benign-leaning
SaProt	LLR -5.91	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.17	GERP -0.58
Regional constraint	o/e 1.05	unconstrained · MANE · 31 kb · p 0.15 · regional, not allelic
Overall
CADD	9.888	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% South Asian · 2/91,062 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000137%

Overall 0.000124% 2/1,613,824 alleles · very rare exomes 1/1,461,600 · genomes 1/152,224 · joint denominator

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: PTCD3
Protein: p.Trp9Arg
Coding: c.25T>C
MANE Select: NM_017952
Type: single nucleotide variant
Location: chr2:86106272 (GRCh38)
Gene constraint: LOEUF 1.132 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.48 · 86 PDB

Full PTCD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PTCD3 p.Trp9Cys Uncertain significance ★ ⚠ same residue
PTCD3 p.Arg524Leu Uncertain significance ★★ ⚠ same condition
PTCD3 p.Pro138Leu Uncertain significance ★★ ⚠ same condition
PTCD3 p.Pro97Ser Uncertain significance ★★ ⚠ same condition
PTCD3 p.Ala109Ser Uncertain significance ★ ⚠ same condition
PTCD3 p.Ala362Ser Uncertain significance ★ ⚠ same condition
PTCD3 p.Ala499Pro Uncertain significance ★ ⚠ same condition
PTCD3 p.Ala568Pro Uncertain significance ★ ⚠ same condition

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/ptcd3-p-trp9arg (accessed [today's date]).

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