Is PPCS p.Gln164= (c.492G>A) pathogenic?

PPCS p.Gln164= (c.492G>A) is classified Benign in PPCS (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-01). Ultra-rare (popmax 0.0788%, amr).

How common is PPCS p.Gln164= (c.492G>A) in the general population?

PPCS p.Gln164= (c.492G>A) is ultra-rare (popmax 0.0788%, amr) (gnomAD).

PPCS p.Gln164=

c.492G>A · rs760329322 · VCV1559467

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0788%, amr)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 3.9	GERP -0.83, phastCons 1
Overall
CADD	7.784	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0788% Admixed American · 47/59,630 alleles

Filtering AF 0.0608% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0545%

Overall 0.003% 48/1,598,090 alleles · ultra-rare exomes 45/1,445,866 · genomes 3/152,224 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0788%	1,269
African / African-American	0.00134%	74,788

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: PPCS
Protein: p.Gln164=
Coding: c.492G>A
MANE Select: NM_024664
dbSNP: rs760329322
Type: single nucleotide variant
Location: chr1:42457057 (GRCh38)

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

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/ppcs-p-gln164 (accessed [today's date]).

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