# NM_001130823.3(DNMT1):c.1389A>G (p.Pro463=)

https://sugi.bio/variant/dnmt1-p-pro463

## Summary

**DNMT1 p.Pro463= (c.1389A>G)** is classified **Benign** in DNMT1 (ClinVar, Multiple submitters, 11 submitters; last evaluated 2026-02-04). Common (popmax 62.8%, eas) — too common for a highly-penetrant pathogenic allele; Associated with autosomal dominant cerebellar ataxia, deafness and narcolepsy.

**At a glance:** Benign · review: Multiple submitters · rsID rs2228611 · 11 submitters · 2 linked conditions · common (popmax 62.8%, eas) — too common for a highly-penetrant pathogenic allele

## For patients & families {#patients}

This is a change in the DNMT1 gene that is classified as benign — not considered disease-causing, submitted by 11 submitters, and is linked to autosomal dominant cerebellar ataxia, deafness and narcolepsy.

*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.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal dominant, Not applicable |
| Age of onset (of this condition) | Adult |
| Clinical trials | 1 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | DNMT1 is a diagnostic-grade gene on 13 Genomics England panels |

**Commonly reported features of Autosomal dominant cerebellar ataxia-deafness-narcolepsy syndrome** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Sensorineural hearing impairment — Very frequent (99-80%)
- Narcolepsy — Very frequent (99-80%)
- Optic atrophy — Frequent (79-30%)
- Abnormality of mitochondrial metabolism — Frequent (79-30%)
- Urinary incontinence — Occasional (29-5%)
- Cataract — Occasional (29-5%)
- Nystagmus — Occasional (29-5%)
- Depression — Occasional (29-5%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0012372/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [DNMT1](https://sugi.bio/atlas/gene/DNMT1/) |
| Protein change (HGVS p.) | p.Pro463= |
| Coding change (HGVS c.) | c.1389A>G |
| MANE Select transcript | [NM_001130823](https://www.ncbi.nlm.nih.gov/nuccore/NM_001130823) |
| dbSNP | [rs2228611](https://www.ncbi.nlm.nih.gov/snp/rs2228611/) |
| Variant type | single nucleotide variant |
| Location | chr19:10156401-10156401 (GRCh38) |
| ClinVar | [VCV257536](https://www.ncbi.nlm.nih.gov/clinvar/variation/257536/) |

**All HGVS expressions:** `LRG_362:g.79886A>G`, `LRG_362t1:c.1389A>G`, `NC_000019.10:g.10156401T>C`, `NC_000019.9:g.10267077T>C`, `NG_028016.3:g.79886A>G`, `NM_001130823.3:c.1389A>G`, `NM_001318730.2:c.1341A>G`, `NM_001318731.2:c.1026A>G`, `NM_001379.4:c.1341A>G`

## Computational & population evidence {#evidence}

**Concordance:** Evidence sources **disagree** — common (popmax 62.8%, eas) — too common for a highly-penetrant pathogenic allele.

- **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 -13.349, GERP -10.5 — fast-evolving / accelerated position
- CADD: **PHRED 0.31**. 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 **62.8%** (eas) · FAF95 62.2% · FAF99 61.9% · 28,046/44,656 in the highest group · 810,084/1,605,870 alleles overall — common (popmax 62.8%, eas) — too common for a highly-penetrant pathogenic allele.

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 62.8% | 2 |
| Middle Eastern | 56% | 2 |
| Amish (not grpmax-eligible) | 55.9% | 2 |
| Ashkenazi Jewish (not grpmax-eligible) | 55.4% | 2 |
| South Asian | 53.8% | 2 |
| Finnish (not grpmax-eligible) | 52.2% | 2 |
| Remaining individuals (not grpmax-eligible) | 51.1% | 2 |
| African / African-American | 50.9% | 2 |
| European (non-Finnish) | 49.5% | 2 |
| Admixed American | 48.5% | 2 |

*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}

**DNMT1** population constraint: LOEUF 0.15, pLI 1, missense-Z 7.3454. *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):

- **autosomal dominant cerebellar ataxia, deafness and narcolepsy** — Definitive (AD)

## Protein context {#protein}

Residue **463** lies in a β-strand; the 'interaction with the prc2/eed-ezh2 complex' region; the rfts domain; the 'homodimerization' region.

AlphaFold model confidence (whole protein): pLDDT 77.88, 47% of residues very-high.

**29 experimental structure(s)** (PDB): [3EPZ](https://www.rcsb.org/structure/3EPZ), [3PTA](https://www.rcsb.org/structure/3PTA), [3SWR](https://www.rcsb.org/structure/3SWR), [4WXX](https://www.rcsb.org/structure/4WXX), [4YOC](https://www.rcsb.org/structure/4YOC), [4Z96](https://www.rcsb.org/structure/4Z96) — incl. mutant structure 9MYS.

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

*Describes the biological roles of DNMT1 (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:** DNMT1's established molecular role includes DNA binding. p.Pro463= falls in the interaction with the prc2/eed-ezh2 complex region. In Reactome, DNMT1 is annotated in disease pathway(s) including **Defective pyroptosis**, **Nuclear events stimulated by ALK signaling in cancer**.

**Disease mechanism (Reactome):** DNMT1 loss or alteration is curated in [Defective pyroptosis](https://reactome.org/content/detail/R-HSA-9710421), [Nuclear events stimulated by ALK signaling in cancer](https://reactome.org/content/detail/R-HSA-9725371).

### Pathways affected {#pathways}

DNMT1 participates in **7 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective pyroptosis](https://reactome.org/content/detail/R-HSA-9710421) | curated |
| ⚕ [Nuclear events stimulated by ALK signaling in cancer](https://reactome.org/content/detail/R-HSA-9725371) | curated |
| [PRC2 methylates histones and DNA](https://reactome.org/content/detail/R-HSA-212300) | curated |
| [STAT3 nuclear events downstream of ALK signaling](https://reactome.org/content/detail/R-HSA-9701898) | curated |
| [SUMOylation of DNA methylation proteins](https://reactome.org/content/detail/R-HSA-4655427) | curated |
| [DNA methylation](https://reactome.org/content/detail/R-HSA-5334118) | electronic |
| [NoRC negatively regulates rRNA expression](https://reactome.org/content/detail/R-HSA-427413) | electronic |

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

**Molecular function:** DNA binding, DNA (cytosine-5-)-methyltransferase activity, DNA-methyltransferase activity, histone H3K18ub reader activity, histone H3K23ub reader activity, histone H3K14ub reader activity.

**Biological process:** positive regulation of gene expression, negative regulation of gene expression, negative regulation of gene expression via chromosomal CpG island methylation, chromosomal DNA methylation maintenance following DNA replication, positive regulation of vascular associated smooth muscle cell proliferation, negative regulation of vascular associated smooth muscle cell apoptotic process.

## Clinical significance {#significance}

**Benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-02-04.

**Submitter consensus:** unanimous (12/12 Benign).

**Submission history:** 12 submissions (2015–2026); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Benign | criteria provided, single submitter | clinical testing | 2015-03-03 |
| Clinical Genetics, Academic Medical Center | Benign | no assertion criteria provided | clinical testing |  |
| Genome-Nilou Lab | Benign | criteria provided, single submitter | clinical testing | 2021-07-30 |
| Blueprint Genetics | Benign | criteria provided, single submitter | clinical testing | 2024-11-28 |
| PreventionGenetics, part of Exact Sciences | Benign | criteria provided, single submitter | clinical testing |  |
| Illumina Laboratory Services, Illumina | Benign | criteria provided, single submitter | clinical testing | 2018-01-13 |
| Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | Benign | no assertion criteria provided | clinical testing |  |
| Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Benign | no assertion criteria provided | clinical testing |  |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |
| Mayo Clinic Laboratories, Mayo Clinic | Benign | criteria provided, single submitter | clinical testing | 2020-06-17 |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-02-04 |

## Associated conditions {#conditions}

[autosomal dominant cerebellar ataxia, deafness and narcolepsy](https://sugi.bio/atlas/disease/autosomal-dominant-cerebellar-ataxia-deafness-and-narcolepsy/), [hereditary sensory neuropathy-deafness-dementia syndrome](https://sugi.bio/atlas/disease/hereditary-sensory-neuropathy-deafness-dementia-syndrome/).

**Reported phenotype names (ClinVar):** Autosomal dominant cerebellar ataxia, deafness and narcolepsy, not specified, Hereditary sensory neuropathy-deafness-dementia syndrome, not provided, Autosomal Dominant Cerebellar Ataxia, Deafness, and Narcolepsy (ADCA-DN), AllHighlyPenetrant, none provided, HSN IE, Hereditary sensory neuropathy type IE, NEUROPATHY, HEREDITARY SENSORY, WITH HEARING LOSS AND DEMENTIA.

## Similar variants {#similar}

Related DNMT1 variant pages (same residue, condition, or type): [DNMT1 p.Ala570Val](/variant/dnmt1-p-ala570val), [DNMT1 p.Tyr511Cys](/variant/dnmt1-p-tyr511cys), [DNMT1 c.1280+2T>C](/variant/dnmt1-c-1280-plus-2t-c), [DNMT1 c.3524-5G>T](/variant/dnmt1-c-3524-minus-5g-t), [DNMT1 c.494-4A>G](/variant/dnmt1-c-494-minus-4a-g), [DNMT1 c.*211G>C](/variant/dnmt1-c-star-211g-c), [DNMT1 c.*253G>A](/variant/dnmt1-c-star-253g-a), [DNMT1 p.Ala1053Thr](/variant/dnmt1-p-ala1053thr).

### 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 257536). 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.*