Is COPA c.3147+19del pathogenic?

COPA c.3147+19del is classified Likely benign in COPA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-11). Associated with autoimmune interstitial lung disease-arthritis syndrome.

What condition is associated with COPA c.3147+19del?

COPA c.3147+19del is associated with autoimmune interstitial lung disease-arthritis syndrome (ClinVar).

COPA c.3147+19del

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

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

VCV4798675

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

autoimmune interstitial lung disease-arthritis syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +19	near-intronic (+19 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.92	GERP -5.4
Non-coding constraint	Z 4.00	1 kb window · o/e 0.71 · regional · uncalibrated

Variant & gene context

Gene: COPA
Coding: c.3147+19del
MANE Select: NM_004371
Type: Deletion
Location: chr1:160291993 (GRCh38)
Gene constraint: LOEUF 0.098 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 83.85 · 3 PDB

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.Asp868del Uncertain significance ★★ same condition
COPA c.387-8del Benign/Likely benign ★★ same condition
COPA p.Gln1045fs Uncertain significance ★ same condition
COPA p.Ile1218fs Uncertain significance ★ same condition
COPA p.Pro1194fs Uncertain significance ★ same condition
COPA p.Pro174del Uncertain significance ★ same condition
COPA c.154+19del Likely benign ★ same condition
COPA c.2263+9_2263+16del Likely benign ★ 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-c-3147-plus-19del (accessed [today's date]).

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