# NM_001012759.3(CTU2):c.736C>A (p.Arg246=)

https://sugi.bio/variant/ctu2-p-arg246

## Summary

**CTU2 p.Arg246= (c.736C>A)** is classified **Likely benign** in CTU2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-15). No allele count reported in gnomAD v4.1 (AN 1,509,668); Associated with CTU2-related disorder.

**At a glance:** Likely benign · review: No assertion criteria · rsID rs767710092 · 1 submitter · 1 linked condition · no allele count reported in gnomAD v4.1 (AN 1,509,668)

## For patients & families {#patients}

This is a change in the CTU2 gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter, and is linked to CTU2-related disorder.

*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 | [CTU2](https://sugi.bio/atlas/gene/CTU2/) |
| Protein change (HGVS p.) | p.Arg246= |
| Coding change (HGVS c.) | c.736C>A |
| MANE Select transcript | [NM_001012759](https://www.ncbi.nlm.nih.gov/nuccore/NM_001012759) |
| dbSNP | [rs767710092](https://www.ncbi.nlm.nih.gov/snp/rs767710092/) |
| Variant type | single nucleotide variant |
| Location | chr16:88712904-88712904 (GRCh38) |
| ClinVar | [VCV3049500](https://www.ncbi.nlm.nih.gov/clinvar/variation/3049500/) |

**All HGVS expressions:** `NC_000016.10:g.88712904C>A`, `NC_000016.9:g.88779312C>A`, `NM_001012759.3:c.736C>A`, `NM_001012762.3:c.736C>A`, `NM_001318507.2:c.949C>A`, `NM_001318513.2:c.475C>A`

## 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 1.559, GERP -1.83, phastCons 0.997 — weakly conserved position
- CADD: **PHRED 11.69**. 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: **no allele count reported in gnomAD v4.1 (AN 1,509,668)** — rarity (ACMG PM2) and BA1/BS1 cannot be assessed for this variant.

*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}

**CTU2** population constraint: LOEUF 1.535, pLI 5.4023e-34, missense-Z -5.9994. *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 80.27, 59% of residues very-high.

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

*Describes the biological roles of CTU2 (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}

CTU2 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [tRNA modification in the nucleus and cytosol](https://reactome.org/content/detail/R-HSA-6782315) | curated |

## Clinical significance {#significance}

**Likely benign** — review status No assertion criteria *(no assertion criteria provided)*, last evaluated 2019-07-15.

**Submitter consensus:** unanimous (1/1 Likely benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| PreventionGenetics, part of Exact Sciences | Likely benign | no assertion criteria provided | clinical testing | 2019-07-15 |

## Associated conditions {#conditions}

[CTU2-related disorder](https://sugi.bio/atlas/disease/ctu2-related-disorder/).

**Reported phenotype names (ClinVar):** CTU2-related disorder, CTU2-related condition.

## Similar variants {#similar}

Related CTU2 variant pages (same residue, condition, or type): [CTU2 p.Arg246Gln](/variant/ctu2-p-arg246gln), [CTU2 p.Arg246Trp](/variant/ctu2-p-arg246trp), [CTU2 p.Thr291=](/variant/ctu2-p-thr291), [CTU2 p.Leu63Pro](/variant/ctu2-p-leu63pro), [CTU2 c.1097+5G>A](/variant/ctu2-c-1097-plus-5g-a), [CTU2 c.1202-8G>A](/variant/ctu2-c-1202-minus-8g-a), [CTU2 c.1353-4G>A](/variant/ctu2-c-1353-minus-4g-a), [CTU2 c.1419+8C>T](/variant/ctu2-c-1419-plus-8c-t).

### 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 3049500). 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.*