# NM_001130823.3(DNMT1):c.4509C>T (p.Pro1503=)

https://sugi.bio/variant/dnmt1-p-pro1503

## Summary

**DNMT1 p.Pro1503= (c.4509C>T)** is classified **Likely benign** in DNMT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-24). Very rare (popmax 0.00445%, eas); Associated with hereditary sensory neuropathy-deafness-dementia syndrome.

**At a glance:** Likely benign · review: Single submitter · rsID rs372868127 · 1 submitter · 1 linked condition · very rare (popmax 0.00445%, eas)

## For patients & families {#patients}

This is a change in the DNMT1 gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter, and is linked to hereditary sensory neuropathy-deafness-dementia syndrome.

*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 |
| Age of onset (of this condition) | Adolescent, Adult |
| Diagnostic panels | DNMT1 is a diagnostic-grade gene on 13 Genomics England panels |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0011927/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.Pro1503= |
| Coding change (HGVS c.) | c.4509C>T |
| MANE Select transcript | [NM_001130823](https://www.ncbi.nlm.nih.gov/nuccore/NM_001130823) |
| dbSNP | [rs372868127](https://www.ncbi.nlm.nih.gov/snp/rs372868127/) |
| Variant type | single nucleotide variant |
| Location | chr19:10136268-10136268 (GRCh38) |
| ClinVar | [VCV1635916](https://www.ncbi.nlm.nih.gov/clinvar/variation/1635916/) |

**All HGVS expressions:** `LRG_362:g.100019C>T`, `NC_000019.10:g.10136268G>A`, `NC_000019.9:g.10246944G>A`, `NG_028016.3:g.100019C>T`, `NM_001130823.3:c.4509C>T`, `NM_001318730.2:c.4470C>T`, `NM_001318731.2:c.4146C>T`, `NM_001379.4:c.4461C>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 -2.729, GERP -2.52 — fast-evolving / accelerated position
- CADD: **PHRED 0.54**. 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: **no splice effect predicted**. SpliceAI outputs four numbers per variant, not one: acceptor loss, donor loss, acceptor gain, donor gain (DS_AL / DS_DL / DS_AG / DS_DG). A loss score is an existing splice site weakened or destroyed; a gain score is a new site created or an existing one strengthened. The release publishes its own filter rule, which we read from the dataset rather than assume: an allele is reported only if the largest of its four deltas reaches 0.2. No allele at this position is in the release, so all four are under 0.2 for every alternate allele here. No figure is shown because none was read: the bound is deduced from that absence. It is a result, not a gap in our data, because the release scores every possible substitution across the transcripts it covers (Ensembl MANE v1.4) before it filters, so what survives for a gene is one continuous stretch. What is measured is that this position sits inside the stretch covered for DNMT1 (1,712 scored positions, the nearest 17 bases away); what is taken from the release's own description, rather than measured, is that coverage inside that stretch is continuous. On that, SpliceAI did score it. *ClinGen's SVI treats the largest of the four as evidence against a splicing effect at or below 0.1, where it may support BP4, and as uninformative between 0.1 and 0.2. We cannot tell which applies here, so these SpliceAI data support neither BP4 nor PP3; that is a statement about this evidence alone, not about the variant's other evidence.*
- Population frequency (gnomAD v4.1): grpmax **0.00445%** (eas) · FAF95 0.000875% · FAF99 0.000474% · 2/44,896 in the highest group · 19/1,613,944 alleles overall — very rare (popmax 0.00445%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.00445% | 22,448 |
| South Asian | 0.00329% | 30,363 |
| Admixed American | 0.00167% | 59,996 |
| European (non-Finnish) | 0.0011% | 90,773 |

*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 **1503** lies in the sam-dependent mtase c5-type domain; the 'interaction with the prc2/eed-ezh2 complex' region; an α-helix.

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.Pro1503= falls in the sam-dependent mtase c5-type domain. 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}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2024-06-24.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2024-06-24 |

## Associated conditions {#conditions}

[hereditary sensory neuropathy-deafness-dementia syndrome](https://sugi.bio/atlas/disease/hereditary-sensory-neuropathy-deafness-dementia-syndrome/).

**Reported phenotype names (ClinVar):** Hereditary sensory neuropathy-deafness-dementia syndrome, Hereditary sensory neuropathy type IE, Hereditary Sensory and Autonomic Neuropathy Type 1E (HSAN1E), NEUROPATHY, HEREDITARY SENSORY, WITH HEARING LOSS AND DEMENTIA, HSN IE.

## 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 2026-10-15); 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 1635916). 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.*