# NM_031938.7(BCO2):c.1228A>T (p.Arg410Trp)

https://sugi.bio/variant/bco2-p-arg410trp

## Summary

**BCO2 p.Arg410Trp (c.1228A>T)** is classified **Uncertain significance** in BCO2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-16). AlphaMissense: likely pathogenic (0.8379); Ultra-rare (popmax 0.0491%, nfe).

**At a glance:** Uncertain significance · review: Single submitter · rsID rs78952668 · 1 submitter · AlphaMissense likely pathogenic · ultra-rare (popmax 0.0491%, nfe)

## For patients & families {#patients}

This is a change in the BCO2 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter.

*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.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [BCO2](https://sugi.bio/atlas/gene/BCO2/) |
| Protein change (HGVS p.) | p.Arg410Trp |
| Coding change (HGVS c.) | c.1228A>T |
| MANE Select transcript | [NM_031938](https://www.ncbi.nlm.nih.gov/nuccore/NM_031938) |
| dbSNP | [rs78952668](https://www.ncbi.nlm.nih.gov/snp/rs78952668/) |
| Variant type | single nucleotide variant |
| Location | chr11:112213757-112213757 (GRCh38) |
| ClinVar | [VCV3133531](https://www.ncbi.nlm.nih.gov/clinvar/variation/3133531/) |

**All HGVS expressions:** `NC_000011.10:g.112213757A>T`, `NC_000011.9:g.112084480A>T`, `NM_001037290.4:c.1126A>T`, `NM_001256397.3:c.1126A>T`, `NM_001256398.3:c.1009A>T`, `NM_001256400.3:c.913A>T`, `NM_031938.7:c.1228A>T`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **damaging** — a triage signal, not a reclassification.

- AlphaMissense **likely pathogenic** (0.8379)
- REVEL 0.922 (moderately pathogenic-leaning) — agrees with AlphaMissense
- SaProt LLR -14.511 (damaging) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this damaging
- SpliceAI predicts **donor loss** (Δ 0.44) — a splice-altering prediction on an uncertain variant — a signal for review
- Conservation: phyloP 4.967, GERP 1.88, phastCons 1 — highly conserved (agrees)
- CADD: **PHRED 26.3**. 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.*
- Regional missense constraint: **o/e 0.97** across the covering region of the MANE Select transcript (112,175,602–112,217,871), spanning 42,269 bp. Chi-square p 0.37. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI deltas (raw): acceptor loss **0.00**, donor loss **0.44**, acceptor gain **0.01**, donor gain **0.00**. Largest is donor loss, 1 bp away.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.01**, donor gain **0.00**.
  Masked SpliceAI — what Ensembl VEP and the Broad lookup serve by default — is below the reporting threshold here, so those tools show **no splice signal** for this allele. Masking zeroes a loss scored against a position that is not an annotated splice site, and a gain that merely strengthens an existing one, so the raw score above is describing a cryptic site rather than the site the variant sits on. *No ACMG code is assigned either way.*
- Population frequency (gnomAD v4.1): grpmax **0.0491%** (nfe) · FAF95 0.0458% · FAF99 0.0444% · 579/1,179,720 in the highest group · 687/1,613,468 alleles overall — ultra-rare (popmax 0.0491%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Finnish (not grpmax-eligible) | 0.127% | 789 |
| European (non-Finnish) (grpmax) | 0.0491% | 2,038 |
| Remaining individuals (not grpmax-eligible) | 0.0272% | 3,675 |
| African / African-American | 0.00935% | 10,701 |
| South Asian | 0.0022% | 45,532 |
| Admixed American | 0.00167% | 59,940 |

Finnish shows a higher raw frequency than the grpmax group. 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.

*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}

**BCO2** population constraint: LOEUF 1.047, pLI 8.0386e-13, missense-Z 0.59178. *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 88.41, 78% of residues very-high.

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

*Describes the biological roles of BCO2 (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.*

**How this variant is thought to act:** BCO2's established molecular role includes oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen.


### Pathways affected {#pathways}

BCO2 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Retinoid metabolism and transport](https://reactome.org/content/detail/R-HSA-975634) | curated |

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

**Molecular function:** oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen.

**Biological process:** carotene metabolic process, carotene catabolic process.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2021-09-16.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2021-09-16 |

**Reported phenotype names (ClinVar):** not specified, AllHighlyPenetrant.

## Similar variants {#similar}

Related BCO2 variant pages (same residue, condition, or type): [BCO2 p.Arg472Ter](/variant/bco2-p-arg472ter), [BCO2 p.Ala115Val](/variant/bco2-p-ala115val), [BCO2 p.Ala223Gly](/variant/bco2-p-ala223gly), [BCO2 p.Ala318Val](/variant/bco2-p-ala318val), [BCO2 p.Ala437Ser](/variant/bco2-p-ala437ser), [BCO2 p.Arg184Trp](/variant/bco2-p-arg184trp), [BCO2 p.Arg253Gln](/variant/bco2-p-arg253gln), [BCO2 p.Arg27Trp](/variant/bco2-p-arg27trp).

### 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 3133531). 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.*