# NM_005138.3(SCO2):c.789T>C (p.Ser263=)

https://sugi.bio/variant/sco2-p-ser263

## Summary

**SCO2 p.Ser263= (c.789T>C)** is classified **Likely benign** in SCO2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-24). Very rare (popmax 0.00223%, eas).

**At a glance:** Likely benign · review: Multiple submitters · rsID rs779010107 · 2 submitters · very rare (popmax 0.00223%, eas)

## For patients & families {#patients}

This is a change in the SCO2 gene that is classified as likely benign — not considered disease-causing, submitted by 2 submitters.

*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 | [SCO2](https://sugi.bio/atlas/gene/SCO2/) |
| Protein change (HGVS p.) | p.Ser263= |
| Coding change (HGVS c.) | c.789T>C |
| MANE Select transcript | [NM_152299](https://www.ncbi.nlm.nih.gov/nuccore/NM_152299) (variant reported on NM_005138) |
| dbSNP | [rs779010107](https://www.ncbi.nlm.nih.gov/snp/rs779010107/) |
| Variant type | single nucleotide variant |
| Location | chr22:50523623-50523623 (GRCh38) |
| ClinVar | [VCV1597355](https://www.ncbi.nlm.nih.gov/clinvar/variation/1597355/) |

**All HGVS expressions:** `NC_000022.10:g.50962052A>G`, `NC_000022.11:g.50523623A>G`, `NG_016235.1:g.7817T>C`, `NG_021419.1:g.20408A>G`, `NM_001169109.2:c.789T>C`, `NM_001169110.1:c.789T>C`, `NM_001169111.2:c.789T>C`, `NM_001185011.2:c.*248A>G`, `NM_005138.3:c.789T>C`, `NM_152299.4:c.*248A>G`

## 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 -5.262, GERP -3.98 — fast-evolving / accelerated position
- CADD: **PHRED 0.041**. 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 looked up on this page** — it was served without the gene's SpliceAI index, so no lookup was made. This is a gap in this page, not in the data, and says nothing about whether a splicing effect is predicted.
- Population frequency (gnomAD v4.1): grpmax **0.00223%** (eas) · FAF95 0.000359% · FAF99 0.00026% · 1/44,880 in the highest group · 12/1,461,222 alleles overall — very rare (popmax 0.00223%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.00223% | 44,880 |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,466 |
| South Asian | 0.0011% | 91,064 |
| European (non-Finnish) | 0.000763% | 131,115 |

*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.*

## Clinical significance {#significance}

**Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2025-07-24.

**Submitter consensus:** unanimous (2/2 Likely benign).

**Submission history:** 2 submissions (2023–2025); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2025-07-24 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2023-10-20 |

**Reported phenotype names (ClinVar):** not provided, not specified, none provided, AllHighlyPenetrant.

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); 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 1597355). 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.*