# NM_014633.5(CTR9):c.741+286del

https://sugi.bio/variant/ctr9-c-741-plus-286del

## Summary

**CTR9 c.741+286del** is classified **Likely benign** in CTR9 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-07). Low-frequency (popmax 3.73%, afr).

**At a glance:** Likely benign · review: Single submitter · rsID rs147350120 · 1 submitter · low-frequency (popmax 3.73%, afr)

## For patients & families {#patients}

This is a change in the CTR9 gene that is classified as likely benign — not considered disease-causing, 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 | [CTR9](https://sugi.bio/atlas/gene/CTR9/) |
| Coding change (HGVS c.) | c.741+286del |
| MANE Select transcript | [NM_014633](https://www.ncbi.nlm.nih.gov/nuccore/NM_014633) |
| dbSNP | [rs147350120](https://www.ncbi.nlm.nih.gov/snp/rs147350120/) |
| Variant type | Deletion |
| Location | chr11:10760595-10760595 (GRCh38) |
| ClinVar | [VCV1317003](https://www.ncbi.nlm.nih.gov/clinvar/variation/1317003/) |

**All HGVS expressions:** `NC_000011.10:g.10760607del`, `NC_000011.9:g.10782154del`, `NG_051671.1:g.14621del`, `NM_001346279.2:c.741+286del`, `NM_014633.5:c.741+286del`

## 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 -0.25, GERP -0.968, phastCons 0.001 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 0.049**. 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.*
- Splice region: **deep intronic (+286 nt into the intron)**.
- Non-coding constraint (Gnocchi): **Z 2.90**, o/e 0.79 (1 kb window 10,760,000–10,761,000). A higher Z means the window carries less variation than expected. Describes the 1 kb window, not this allele. No ClinGen expert panel references Gnocchi and no ACMG-calibrated threshold exists for it. *Descriptive; no cut-point applied.*
- SpliceAI: **not assessed** — the release is built from a substitutions-only source, so it holds no deletion variants. That is a property of the dataset, not of the variant, and is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **3.73%** (afr) · FAF95 3.57% · FAF99 3.5% · 1,396/37,398 in the highest group · 1,541/130,692 alleles overall — low-frequency (popmax 3.73%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 3.73% | 27 |
| Remaining individuals (not grpmax-eligible) | 0.664% | 150 |
| Finnish (not grpmax-eligible) | 0.459% | 218 |
| Admixed American | 0.425% | 235 |
| East Asian | 0.135% | 742 |
| European (non-Finnish) | 0.0678% | 1,474 |

*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}

**CTR9** population constraint: LOEUF 0.368, pLI 1, missense-Z 4.7753. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **CTR9-related neurodevelopmental disorder** — Moderate (AD)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 76.62, 43% of residues very-high.

**21 experimental structure(s)** (PDB): [5ZYQ](https://www.rcsb.org/structure/5ZYQ), [6GMH](https://www.rcsb.org/structure/6GMH), [6TED](https://www.rcsb.org/structure/6TED), [7OOP](https://www.rcsb.org/structure/7OOP), [7OPC](https://www.rcsb.org/structure/7OPC), [7OPD](https://www.rcsb.org/structure/7OPD).

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

*Describes the biological roles of CTR9 (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:** CTR9 participates in disease-associated pathways. In Reactome, CTR9 is annotated in disease pathway(s) including **Dengue virus activates/modulates innate and adaptive immune responses**.

**Disease mechanism (Reactome):** CTR9 loss or alteration is curated in [Dengue virus activates/modulates innate and adaptive immune responses](https://reactome.org/content/detail/R-HSA-9920588).

### Pathways affected {#pathways}

CTR9 participates in **7 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Dengue virus activates/modulates innate and adaptive immune responses](https://reactome.org/content/detail/R-HSA-9920588) | curated |
| [CHD1 and CHD2 subfamily](https://reactome.org/content/detail/R-HSA-9943411) | curated |
| [E3 ubiquitin ligases ubiquitinate target proteins](https://reactome.org/content/detail/R-HSA-8866654) | curated |
| [Formation of RNA Pol II elongation complex ](https://reactome.org/content/detail/R-HSA-112382) | curated |
| [RNA Polymerase II Pre-transcription Events](https://reactome.org/content/detail/R-HSA-674695) | curated |
| [RNA Polymerase II Transcription Elongation](https://reactome.org/content/detail/R-HSA-75955) | curated |
| [Somatic hypermutation of immunoglobulin genes](https://reactome.org/content/detail/R-HSA-9938024) | electronic |

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

**Biological process:** transcription elongation by RNA polymerase II, stem cell population maintenance, negative regulation of myeloid cell differentiation, positive regulation of transcription by RNA polymerase II.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2019-08-07.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Likely benign | criteria provided, single submitter | clinical testing | 2019-08-07 |

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

## Similar variants {#similar}

Related CTR9 variant pages (same residue, condition, or type): [CTR9 p.Ala198fs](/variant/ctr9-p-ala198fs), [CTR9 p.Asp771fs](/variant/ctr9-p-asp771fs), [CTR9 p.Ile6fs](/variant/ctr9-p-ile6fs), [CTR9 p.Leu733del](/variant/ctr9-p-leu733del), [CTR9 p.Lys958_Lys959del](/variant/ctr9-p-lys958-lys959del), [CTR9 c.1194+15del](/variant/ctr9-c-1194-plus-15del), [CTR9 c.1687-137del](/variant/ctr9-c-1687-minus-137del), [CTR9 c.2373-23_2373-19del](/variant/ctr9-c-2373-minus-23-2373-minus-19del).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); 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 2026-10-14); 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 1317003). 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.*