Is PTCD3 p.Ala179= (c.537A>G) pathogenic?

PTCD3 p.Ala179= (c.537A>G) is classified Uncertain significance in PTCD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-13). No allele count reported in gnomAD v4.1 (AN 1,613,390).

How common is PTCD3 p.Ala179= (c.537A>G) in the general population?

PTCD3 p.Ala179= (c.537A>G) is no allele count reported in gnomAD v4.1 (AN 1,613,390) (gnomAD).

PTCD3 p.Ala179=

c.537A>G · VCV4955842

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,390)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.30	donor loss · deltas
Pangolin	Δ0.56	loss · gain 0.03 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 11	GERP 2.1, phastCons 1
Overall
CADD	21.6	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,390). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PTCD3
Protein: p.Ala179=
Coding: c.537A>G
MANE Select: NM_017952
Type: single nucleotide variant
Location: chr2:86119043 (GRCh38)
Gene constraint: LOEUF 1.132 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.48 · 86 PDB
Residue 179: an α-helix

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

Similar variants

PTCD3 p.Arg524Leu Uncertain significance ★★ ⚠ same type
PTCD3 p.Phe447Tyr Uncertain significance ★★ ⚠ same type
PTCD3 p.Pro138Leu Uncertain significance ★★ ⚠ same type
PTCD3 p.Pro97Ser Uncertain significance ★★ ⚠ same type
PTCD3 c.1148-2A>G Likely pathogenic ★ same type
PTCD3 c.1630-1G>A Likely pathogenic ★ same type
PTCD3 c.1979+1G>A Likely pathogenic ★ same type
PTCD3 c.805-2A>G Likely pathogenic ★ 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/ptcd3-p-ala179 (accessed [today's date]).

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