Is COPZ1 p.Asp32= (c.96C>T) pathogenic?

COPZ1 p.Asp32= (c.96C>T) is classified Likely benign in COPZ1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-21). Ultra-rare (popmax 0.01%, amr).

How common is COPZ1 p.Asp32= (c.96C>T) in the general population?

COPZ1 p.Asp32= (c.96C>T) is ultra-rare (popmax 0.01%, amr) (gnomAD).

COPZ1 p.Asp32=

c.96C>T · rs768230114 · VCV3076296

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.01%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.039	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.9	GERP 0.018
Overall
CADD	11.61	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.01% Admixed American · 6/59,992 alleles

Filtering AF 0.00428% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00295%

Overall 0.00329% 53/1,612,504 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.01%	9,999
African / African-American	0.00401%	24,954
European (non-Finnish)	0.00339%	29,467
Remaining individualsnot grpmax-eligible	0.0032%	31,224
South Asian	0.0022%	45,527

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: COPZ1
Protein: p.Asp32=
Coding: c.96C>T
MANE Select: NM_016057
dbSNP: rs768230114
Type: single nucleotide variant
Location: chr12:54342214 (GRCh38)
Gene constraint: LOEUF 0.443 · pLI 0.99 (gnomAD)
Structure: AlphaFold pLDDT 89.37 · 2 PDB
Residue 32: a β-strand

Full COPZ1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COPZ1 p.Thr159= Benign ★★ same type
COPZ1 p.Ala167Thr Uncertain significance ★ ⚠ same type
COPZ1 p.Ala43Val Uncertain significance ★ ⚠ same type
COPZ1 p.Arg112Gln Uncertain significance ★ ⚠ same type
COPZ1 p.Arg145Gln Uncertain significance ★ ⚠ same type
COPZ1 p.Arg145Trp Uncertain significance ★ ⚠ same type
COPZ1 p.Arg25Gln Uncertain significance ★ ⚠ same type
COPZ1 p.Asn21Lys 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/copz1-p-asp32 (accessed [today's date]).

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