# NM_003863.4(DPM2):c.74C>G (p.Thr25Ser)

https://sugi.bio/variant/dpm2-p-thr25ser

## Summary

**DPM2 p.Thr25Ser (c.74C>G)** is classified **Uncertain significance** in DPM2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-04). AlphaMissense: likely benign (0.1634); Ultra-rare (popmax 0.0187%, afr); Associated with congenital muscular dystrophy with intellectual disability and severe epilepsy.

**At a glance:** Uncertain significance · review: Single submitter · rsID rs1026866240 · 1 submitter · 1 linked condition · AlphaMissense likely benign · ultra-rare (popmax 0.0187%, afr)

## For patients & families {#patients}

This is a change in the DPM2 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter, and is linked to congenital muscular dystrophy with intellectual disability and severe epilepsy.

*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 recessive |
| Age of onset (of this condition) | Infancy, Neonatal |
| Diagnostic panels | DPM2 is a diagnostic-grade gene on 10 Genomics England panels |

**Commonly reported features of Congenital muscular dystrophy with intellectual disability and severe epilepsy** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Progressive microcephaly — Frequent (79-30%)
- Micrognathia — Frequent (79-30%)
- Osteopenia — Frequent (79-30%)
- Global developmental delay — Frequent (79-30%)
- Generalized hypotonia — Frequent (79-30%)
- Cerebellar hypoplasia — Frequent (79-30%)
- Absent speech — Frequent (79-30%)
- Failure to thrive — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0012416/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [DPM2](https://sugi.bio/atlas/gene/DPM2/) |
| Protein change (HGVS p.) | p.Thr25Ser |
| Coding change (HGVS c.) | c.74C>G |
| MANE Select transcript | [NM_003863](https://www.ncbi.nlm.nih.gov/nuccore/NM_003863) |
| dbSNP | [rs1026866240](https://www.ncbi.nlm.nih.gov/snp/rs1026866240/) |
| Variant type | single nucleotide variant |
| Location | chr9:127937453-127937453 (GRCh38) |
| ClinVar | [VCV1419961](https://www.ncbi.nlm.nih.gov/clinvar/variation/1419961/) |

**All HGVS expressions:** `NC_000009.11:g.130699732G>C`, `NC_000009.12:g.127937453G>C`, `NG_032927.1:g.6032C>G`, `NM_001378436.1:c.74C>G`, `NM_001378437.1:c.3+365C>G`, `NM_003863.4:c.74C>G`, `NR_165631.1:n.108C>G`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **tolerated** — a triage signal, not a reclassification.

- AlphaMissense **likely benign** (0.1634)
- REVEL 0.174 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -5.049 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP 9.754, GERP 0.798, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 24.4**. 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.*
- Regional missense constraint: **o/e 0.91** across the covering region of the MANE Select transcript (127,935,725–127,937,820), spanning 2,095 bp. Chi-square p 0.35. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code 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 **0.0187%** (afr) · FAF95 0.0112% · FAF99 0.00905% · 14/74,920 in the highest group · 15/1,613,558 alleles overall — ultra-rare (popmax 0.0187%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 0.0187% | 5,351 |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,462 |

*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}

**DPM2** population constraint: LOEUF 1.274, pLI 0.013762, missense-Z 0.045509. *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):

- **congenital muscular dystrophy with intellectual disability and severe epilepsy** — Moderate (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 91.96, 85% of residues very-high.

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

*Describes the biological roles of DPM2 (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:** DPM2's established molecular role includes enzyme activator activity. In Reactome, DPM2 is annotated in disease pathway(s) including **Defective DPM1 causes DPM1-CDG**, **Defective DPM2 causes DPM2-CDG**.

**Disease mechanism (Reactome):** DPM2 loss or alteration is curated in [Defective DPM1 causes DPM1-CDG](https://reactome.org/content/detail/R-HSA-4717374), [Defective DPM2 causes DPM2-CDG](https://reactome.org/content/detail/R-HSA-4719377), [Defective DPM3 causes DPM3-CDG](https://reactome.org/content/detail/R-HSA-4719360).

### Pathways affected {#pathways}

DPM2 participates in **6 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective DPM1 causes DPM1-CDG](https://reactome.org/content/detail/R-HSA-4717374) | curated |
| ⚕ [Defective DPM2 causes DPM2-CDG](https://reactome.org/content/detail/R-HSA-4719377) | curated |
| ⚕ [Defective DPM3 causes DPM3-CDG](https://reactome.org/content/detail/R-HSA-4719360) | curated |
| ⚕ [Maturation of DENV proteins](https://reactome.org/content/detail/R-HSA-9918432) | curated |
| [Synthesis of dolichyl-phosphate mannose](https://reactome.org/content/detail/R-HSA-162699) | curated |
| [Synthesis of glycosylphosphatidylinositol (GPI)](https://reactome.org/content/detail/R-HSA-162710) | curated |

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

**Molecular function:** enzyme activator activity.

**Biological process:** GPI anchor biosynthetic process, dolichyl monophosphate biosynthetic process, dolichol phosphate mannose biosynthetic process.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2022-03-04.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2022-03-04 |

## Associated conditions {#conditions}

[congenital muscular dystrophy with intellectual disability and severe epilepsy](https://sugi.bio/atlas/disease/congenital-muscular-dystrophy-with-intellectual-disability-and-severe-epilepsy/).

**Reported phenotype names (ClinVar):** Congenital muscular dystrophy with intellectual disability and severe epilepsy, Congenital disorder of glycosylation type 1u, CDG Iu.

## Similar variants {#similar}

Related DPM2 variant pages (same residue, condition, or type): [DPM2 p.Arg47Ter](/variant/dpm2-p-arg47ter), [DPM2 p.Ala52Thr](/variant/dpm2-p-ala52thr), [DPM2 p.Leu30Val](/variant/dpm2-p-leu30val), [DPM2 p.Leu62Val](/variant/dpm2-p-leu62val), [DPM2 p.Tyr43His](/variant/dpm2-p-tyr43his), [DPM2 p.Val51Ile](/variant/dpm2-p-val51ile), [DPM2 c.3+12A>G](/variant/dpm2-c-3-plus-12a-g), [DPM2 c.94-8G>T](/variant/dpm2-c-94-minus-8g-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 1419961). 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.*