# NM_004371.4(COPA):c.1741C>T (p.Leu581=)

https://sugi.bio/variant/copa-p-leu581

## Summary

**COPA p.Leu581= (c.1741C>T)** is classified **Benign/Likely benign** in COPA (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-03-31). Low-frequency (popmax 3.49%, nfe); Associated with autoimmune interstitial lung disease-arthritis syndrome.

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs79304843 · 8 submitters · 1 linked condition · low-frequency (popmax 3.49%, nfe)

## For patients & families {#patients}

This is a change in the COPA gene that is classified as benign/likely benign — not considered disease-causing, submitted by 8 submitters, and is linked to autoimmune interstitial lung disease-arthritis syndrome.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal dominant |
| Age of onset (of this condition) | Childhood, Infancy |
| Diagnostic panels | COPA is a diagnostic-grade gene on 4 Genomics England panels |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0017762/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [COPA](https://sugi.bio/atlas/gene/COPA/) |
| Protein change (HGVS p.) | p.Leu581= |
| Coding change (HGVS c.) | c.1741C>T |
| MANE Select transcript | [NM_004371](https://www.ncbi.nlm.nih.gov/nuccore/NM_004371) |
| dbSNP | [rs79304843](https://www.ncbi.nlm.nih.gov/snp/rs79304843/) |
| Variant type | single nucleotide variant |
| Location | chr1:160299191-160299191 (GRCh38) |
| ClinVar | [VCV476022](https://www.ncbi.nlm.nih.gov/clinvar/variation/476022/) |

**All HGVS expressions:** `LRG_1336:g.49374C>T`, `LRG_1336t1:c.1741C>T`, `NC_000001.10:g.160268981G>A`, `NC_000001.11:g.160299191G>A`, `NG_050927.1:g.49374C>T`, `NM_001098398.2:c.1768C>T`, `NM_004371.4:c.1741C>T`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 7.568, GERP 1.79, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 11.67**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **3.49%** (nfe) · FAF95 3.46% · FAF99 3.45% · 41,183/1,180,004 in the highest group · 50,227/1,614,114 alleles overall — low-frequency (popmax 3.49%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| European (non-Finnish) (grpmax) | 3.49% | 29 |
| Middle Eastern | 3.23% | 31 |
| South Asian | 3.17% | 32 |
| Ashkenazi Jewish (not grpmax-eligible) | 2.86% | 35 |
| Remaining individuals (not grpmax-eligible) | 2.84% | 35 |
| Amish (not grpmax-eligible) | 2.19% | 46 |
| Finnish (not grpmax-eligible) | 1.95% | 51 |
| Admixed American | 1.63% | 61 |
| African / African-American | 1.45% | 69 |
| East Asian | 0.0111% | 8,977 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**COPA** population constraint: LOEUF 0.098, pLI 1, missense-Z 4.8017. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 83.85, 46% of residues very-high.

**3 experimental structure(s)** (PDB): [6PBG](https://www.rcsb.org/structure/6PBG), [6TZT](https://www.rcsb.org/structure/6TZT), [6U3V](https://www.rcsb.org/structure/6U3V).

## What this gene does {#gene-function}

*Describes the biological roles of COPA (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*


### Pathways affected {#pathways}

COPA participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [COPI-dependent Golgi-to-ER retrograde traffic](https://reactome.org/content/detail/R-HSA-6811434) | curated |
| [COPI-mediated anterograde transport](https://reactome.org/content/detail/R-HSA-6807878) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Biological process:** pancreatic juice secretion.

## Clinical significance {#significance}

**Benign/Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-03-31.

**Submitter consensus:** conflicting (6 Benign, 1 not provided, 1 Likely benign).

**Submission history:** 8 submissions (2023–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | Benign | no assertion criteria provided | clinical testing |  |
| Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Benign | no assertion criteria provided | clinical testing |  |
| GenomeConnect, ClinGen | not provided | no classification provided | phenotyping only |  |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-02-03 |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |
| Mayo Clinic Laboratories, Mayo Clinic | Benign | criteria provided, single submitter | clinical testing | 2023-09-21 |
| Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Benign | criteria provided, single submitter | clinical testing | 2026-03-31 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-11-26 |

## Associated conditions {#conditions}

[autoimmune interstitial lung disease-arthritis syndrome](https://sugi.bio/atlas/disease/autoimmune-interstitial-lung-disease-arthritis-syndrome/).

**Reported phenotype names (ClinVar):** Autoimmune interstitial lung disease-arthritis syndrome, not specified, not provided, Autoinflammation and autoimmunity, systemic, with immune dysregulation, none provided, AllHighlyPenetrant.

## Same-residue context {#hotspot}

Residue **581** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [COPA p.Leu581Gln](/variant/copa-p-leu581gln). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related COPA variant pages (same residue, condition, or type): [COPA p.Leu581Gln](/variant/copa-p-leu581gln), [COPA p.Arg233His](/variant/copa-p-arg233his), [COPA p.Glu241Lys](/variant/copa-p-glu241lys), [COPA p.Ala111Thr](/variant/copa-p-ala111thr), [COPA p.Ala176Val](/variant/copa-p-ala176val), [COPA p.Ala407Val](/variant/copa-p-ala407val), [COPA p.Ala422Thr](/variant/copa-p-ala422thr), [COPA p.Ala469Val](/variant/copa-p-ala469val).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 476022). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*