Is COPA p.Ser895Ala (c.2683T>G) pathogenic?

COPA p.Ser895Ala (c.2683T>G) is classified Conflicting classifications of pathogenicity in COPA (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2026-02-01). AlphaMissense: likely benign (0.0627); Rare (popmax 0.107%, afr); Associated with autoimmune interstitial lung disease-arthritis syndrome.

What condition is associated with COPA p.Ser895Ala (c.2683T>G)?

COPA p.Ser895Ala (c.2683T>G) is associated with autoimmune interstitial lung disease-arthritis syndrome (ClinVar).

How common is COPA p.Ser895Ala (c.2683T>G) in the general population?

COPA p.Ser895Ala (c.2683T>G) is rare (popmax 0.107%, afr) (gnomAD).

What do computational predictors say about COPA p.Ser895Ala (c.2683T>G)?

AlphaMissense predicts likely benign (score 0.0627) — an in-silico prediction, not a clinical call.

COPA p.Ser895Ala

Q: How is Autoimmune interstitial lung disease-arthritis syndrome inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

c.2683T>G · rs139398871 · VCV542649

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.0627 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.107%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

autoimmune interstitial lung disease-arthritis syndrome

Computational evidence

Protein change
AlphaMissense	0.0627	likely benign
REVEL	0.023	moderately benign-leaning
SaProt	LLR -3.85	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.96	GERP 0.001, phastCons 0.43
Regional constraint	o/e 0.72	unconstrained · MANE · 42 kb · p 1.1e-24 · regional, not allelic
Overall
CADD	13.92	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.107% African / African-American · 78/73,156 alleles

Filtering AF 0.0876% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0805%

Overall 0.00584% 93/1,592,658 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.107%	938
Remaining individualsnot grpmax-eligible	0.00974%	10,270
South Asian	0.00459%	21,781
European (non-Finnish)	0.000426%	234,672

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: COPA
Protein: p.Ser895Ala
Coding: c.2683T>G
MANE Select: NM_004371
dbSNP: rs139398871
Type: single nucleotide variant
Location: chr1:160293457 (GRCh38)
Gene constraint: LOEUF 0.098 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 83.85 · 3 PDB
Residue 895: a modified residue (phosphoserine)

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

Disease context

autoimmune interstitial lung disease-arthritis syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autoimmune interstitial lung disease-arthritis syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: Childhood, Infancy

Similar variants

COPA p.Ser895Phe Uncertain significance ★ ⚠ same residue
COPA p.Arg233His Pathogenic/Likely pathogenic ★★ same condition
COPA p.Glu241Lys Pathogenic ★★ same condition
COPA p.Ala111Thr Uncertain significance ★★ ⚠ same condition
COPA p.Ala176Val Uncertain significance ★★ ⚠ same condition
COPA p.Ala407Val Uncertain significance ★★ ⚠ same condition
COPA p.Ala422Thr Uncertain significance ★★ ⚠ same condition
COPA p.Ala469Val Uncertain significance ★★ ⚠ same condition

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/copa-p-ser895ala (accessed [today's date]).

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