Sugi Variant
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COPS2/p.Arg162Gln

COPS2 p.Arg162Gln

c.485G>A · rs376675090 · VCV2221949

Uncertain significance Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely benign
0.1831 · ACMG-weighted
gnomAD v4.1
Rare
very rare (popmax 0.00224%, eas)
Missense predictors
0/2 damaging
AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense0.1831likely benign
REVEL0.324indeterminate
SaProtLLR -8.23tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI—not assessed · no allele here is in the release
Constraint at this position
ConservationphyloP 7.7GERP 1.9, phastCons 1
Regional constrainto/e 0.40unconstrained · MANE · 21 kb · p 2.2e-19 · regional, not allelic
Overall
CADD23.8PHRED · 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 0.00224% East Asian · 1/44,736 alleles
Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%
Overall 0.000686% 11/1,604,662 alleles · very rare exomes 9/1,452,670 · genomes 2/151,992 · joint denominator
Ancestry group Frequency 1 in
Ashkenazi Jewishnot grpmax-eligible 0.0102% 9,804
East Asiangrpmax 0.00224% 44,736
Remaining individualsnot grpmax-eligible 0.00161% 62,144
African / African-American 0.00135% 74,308
European (non-Finnish) 0.000425% 235,412

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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
COPS2
Protein
p.Arg162Gln
Coding
c.485G>A
MANE Select
NM_004236
dbSNP
rs376675090
Type
single nucleotide variant
Location
chr15:49137205 (GRCh38)
Gene constraint
LOEUF 0.138 · pLI 1.00 (gnomAD)
Structure
AlphaFold pLDDT 85.22 · 29 PDB
Residue 162
an α-helix; the 'mediates interaction with nif3l1' region
Full COPS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

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/cops2-p-arg162gln (accessed [today's date]).

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