Is COPB1 p.Pro15= (c.45A>G) pathogenic?

COPB1 p.Pro15= (c.45A>G) is classified Likely benign in COPB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-01). Ultra-rare (popmax 0.099%, sas).

How common is COPB1 p.Pro15= (c.45A>G) in the general population?

COPB1 p.Pro15= (c.45A>G) is ultra-rare (popmax 0.099%, sas) (gnomAD).

COPB1 p.Pro15=

c.45A>G · rs368221445 · VCV3025546

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.099%, sas)

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 -0.27	GERP 0.067, phastCons 0.36
Overall
CADD	12.3	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.099% South Asian · 89/89,876 alleles

Filtering AF 0.0823% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0762%

Overall 0.0154% 248/1,610,936 alleles · ultra-rare exomes 227/1,458,710 · genomes 21/152,226 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.099%	1,010
Remaining individualsnot grpmax-eligible	0.0176%	5,673
European (non-Finnish)	0.012%	8,363
East Asian	0.00669%	14,937
Admixed American	0.00335%	29,861
Finnishnot grpmax-eligible	0.00157%	63,654
African / African-American	0.00133%	74,932

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: COPB1
Protein: p.Pro15=
Coding: c.45A>G
MANE Select: NM_001144061
dbSNP: rs368221445
Type: single nucleotide variant
Location: chr11:14498884 (GRCh38)
Gene constraint: LOEUF 0.269 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 82.55

Full COPB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COPB1 p.Met16Val Uncertain significance ★★ ⚠ same type
COPB1 p.Ser410Arg Uncertain significance ★★ ⚠ same type
COPB1 c.958-4T>G Likely benign ★★ same type
COPB1 p.Leu271= Likely benign ★★ same type
COPB1 p.Phe551Val Pathogenic ★ same type
COPB1 c.1455+2T>C Uncertain significance ★ same type
COPB1 c.1616+2T>C Uncertain significance ★ same type
COPB1 c.-57-2A>G Conflicting classifications of pathogenicity ★ ⚠ 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/copb1-p-pro15 (accessed [today's date]).

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