# NM_005782.4(ALYREF):c.46C>T (p.Leu16=)

https://sugi.bio/variant/alyref-p-leu16

## Summary

**ALYREF p.Leu16= (c.46C>T)** is classified **Likely benign** in ALYREF (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-03-11). Ultra-rare (popmax 0.0369%, amr); Associated with ALYREF-related disorder.

**At a glance:** Likely benign · review: No assertion criteria · 1 submitter · 1 linked condition · ultra-rare (popmax 0.0369%, amr)

## For patients & families {#patients}

This is a change in the ALYREF gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter, and is linked to ALYREF-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 | [ALYREF](https://sugi.bio/atlas/gene/ALYREF/) |
| Protein change (HGVS p.) | p.Leu16= |
| Coding change (HGVS c.) | c.46C>T |
| MANE Select transcript | [NM_005782](https://www.ncbi.nlm.nih.gov/nuccore/NM_005782) |
| Variant type | single nucleotide variant |
| Location | chr17:81891535-81891535 (GRCh38) |
| ClinVar | [VCV3350262](https://www.ncbi.nlm.nih.gov/clinvar/variation/3350262/) |

**All HGVS expressions:** `NC_000017.10:g.79849411G>A`, `NC_000017.11:g.81891535G>A`, `NG_197067.1:g.33G>A`, `NM_001289414.1:c.-75+684G>A`, `NM_005782.4:c.46C>T`, `NR_158770.1:n.53C>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 1.824, GERP -1.06, phastCons 1 — weakly conserved position
- CADD: **PHRED 11.23**. 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 **0.0369%** (amr) · FAF95 0.0226% · FAF99 0.0183% · 15/40,674 in the highest group · 16/1,283,626 alleles overall — ultra-rare (popmax 0.0369%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Admixed American (grpmax) | 0.0369% | 2,712 |
| Remaining individuals (not grpmax-eligible) | 0.00185% | 53,976 |

*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}

**ALYREF** population constraint: LOEUF 0.235, pLI 0.99971, missense-Z -0.1749. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **16** lies in the 'disordered' region; the 'rna-binding domain 1' region; the 'sufficient for rna-binding, interaction with nxf1-nxt1 heterodimer' region.

AlphaFold model confidence (whole protein): pLDDT 65.65, 25% of residues very-high.

**4 experimental structure(s)** (PDB): [3ULH](https://www.rcsb.org/structure/3ULH), [7ZNJ](https://www.rcsb.org/structure/7ZNJ), [7ZNK](https://www.rcsb.org/structure/7ZNK), [8R7L](https://www.rcsb.org/structure/8R7L).

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

*Describes the biological roles of ALYREF (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:** ALYREF's established molecular role includes RNA binding. p.Leu16= falls in the disordered region. In Reactome, ALYREF is annotated in disease pathway(s) including **Dengue Virus-Host Interactions**.

**Disease mechanism (Reactome):** ALYREF loss or alteration is curated in [Dengue Virus-Host Interactions](https://reactome.org/content/detail/R-HSA-9918481).

### Pathways affected {#pathways}

ALYREF participates in **8 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Dengue Virus-Host Interactions](https://reactome.org/content/detail/R-HSA-9918481) | other |
| [RNA Polymerase II Transcription Termination](https://reactome.org/content/detail/R-HSA-73856) | other |
| [Transport of Mature mRNA Derived from an Intronless Transcript](https://reactome.org/content/detail/R-HSA-159231) | other |
| [Transport of Mature mRNA derived from an Intron-Containing Transcript](https://reactome.org/content/detail/R-HSA-159236) | other |
| [Transport of the SLBP Dependant Mature mRNA](https://reactome.org/content/detail/R-HSA-159230) | other |
| [Transport of the SLBP independent Mature mRNA](https://reactome.org/content/detail/R-HSA-159227) | other |
| [mRNA 3'-end processing](https://reactome.org/content/detail/R-HSA-72187) | other |
| [mRNA Splicing - Major Pathway](https://reactome.org/content/detail/R-HSA-72163) | other |

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

**Molecular function:** RNA binding, C5-methylcytidine-containing RNA reader activity.

**Biological process:** osteoblast differentiation, RNA export from nucleus, mRNA export from nucleus, mRNA metabolic process.

## Clinical significance {#significance}

**Likely benign** — review status No assertion criteria *(no assertion criteria provided)*, last evaluated 2024-03-11.

**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 | 2024-03-11 |

## Associated conditions {#conditions}

[ALYREF-related disorder](https://sugi.bio/atlas/disease/alyref-related-disorder/).

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

## Similar variants {#similar}

Related ALYREF variant pages (same residue, condition, or type): [ALYREF p.Pro2His](/variant/alyref-p-pro2his), [ALYREF p.Arg231Leu](/variant/alyref-p-arg231leu), [ALYREF p.Gln253Glu](/variant/alyref-p-gln253glu), [ALYREF p.Ser4Phe](/variant/alyref-p-ser4phe), [ALYREF p.Ser201=](/variant/alyref-p-ser201).

### 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 3350262). 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.*