Is COPA p.Phe457del (c.1367TCT[1]) pathogenic?

COPA p.Phe457del (c.1367TCT[1]) is classified Uncertain significance in COPA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-18). No gnomAD frequency available for this variant; Associated with autoimmune interstitial lung disease-arthritis syndrome.

What condition is associated with COPA p.Phe457del (c.1367TCT[1])?

COPA p.Phe457del (c.1367TCT[1]) is associated with autoimmune interstitial lung disease-arthritis syndrome (ClinVar).

How common is COPA p.Phe457del (c.1367TCT[1]) in the general population?

COPA p.Phe457del (c.1367TCT[1]) is no gnomAD frequency available for this variant (gnomAD).

COPA p.Phe457del

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.1367TCT[1] · rs2101837675 · VCV1365359

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.8	GERP 2.6, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: COPA
Protein: p.Phe457del
Coding: c.1367TCT[1]
MANE Select: NM_004371
dbSNP: rs2101837675
Type: Microsatellite
Location: chr1:160306424 (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.835ID[1] Uncertain significance ★ same condition
COPA p.Glu884del Uncertain significance ★ same condition
COPA p.Gly829del Uncertain significance ★ same condition
COPA c.1443-7_1443-4del Likely benign ★ same condition
COPA c.2677-24_2677-18del Likely benign ★ same condition
COPA c.3616-12_3616-9del Likely benign ★ same condition
COPA p.Arg233His Pathogenic/Likely pathogenic ★★ same condition
COPA p.Glu241Lys Pathogenic ★★ 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-phe457del (accessed [today's date]).

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