# NM_000290.4(PGAM2):c.459C>T (p.Cys153=)

https://sugi.bio/variant/pgam2-p-cys153

## Summary

**PGAM2 p.Cys153= (c.459C>T)** is classified **Conflicting classifications of pathogenicity** in PGAM2 (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2026-06-01). Rare (popmax 0.169%, nfe); Associated with glycogen storage disease due to phosphoglycerate mutase deficiency.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs143809043 · 7 submitters · 1 linked condition · rare (popmax 0.169%, nfe)

## For patients & families {#patients}

This is a change in the PGAM2 gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 7 submitters, and is linked to glycogen storage disease due to phosphoglycerate mutase deficiency.

*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) | Adolescent, Childhood |
| Clinical trials | 1 registered for this condition — see ClinicalTrials.gov |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0009964/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PGAM2](https://sugi.bio/atlas/gene/PGAM2/) |
| Protein change (HGVS p.) | p.Cys153= |
| Coding change (HGVS c.) | c.459C>T |
| MANE Select transcript | [NM_001014436](https://www.ncbi.nlm.nih.gov/nuccore/NM_001014436) (variant reported on NM_000290) |
| dbSNP | [rs143809043](https://www.ncbi.nlm.nih.gov/snp/rs143809043/) |
| Variant type | single nucleotide variant |
| Location | chr7:44064968-44064968 (GRCh38) |
| ClinVar | [VCV360272](https://www.ncbi.nlm.nih.gov/clinvar/variation/360272/) |

**All HGVS expressions:** `NC_000007.13:g.44104567G>A`, `NC_000007.14:g.44064968G>A`, `NG_013016.1:g.5620C>T`, `NG_177787.1:g.165G>A`, `NM_000290.4:c.459C>T`, `NM_001014436.3:c.*4052G>A`, `NM_001122956.2:c.*4052G>A`, `NM_001284313.2:c.*4052G>A`, `NM_001284315.2:c.*4052G>A`, `NM_001362723.2:c.*4052G>A`, `NM_014063.7:c.*4052G>A`

## 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 -8.863, GERP -3.69 — fast-evolving / accelerated position
- CADD: **PHRED 1.671**. 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 looked up on this page** — it was served without the gene's SpliceAI index, so no lookup was made. This is a gap in this page, not in the data, and says nothing about whether a splicing effect is predicted.
- Population frequency (gnomAD v4.1): grpmax **0.169%** (nfe) · FAF95 0.163% · FAF99 0.16% · 1,994/1,179,606 in the highest group · 2,134/1,607,600 alleles overall — rare (popmax 0.169%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| European (non-Finnish) (grpmax) | 0.169% | 592 |
| Remaining individuals (not grpmax-eligible) | 0.0929% | 1,077 |
| Admixed American | 0.0735% | 1,361 |
| Middle Eastern | 0.0496% | 2,017 |
| African / African-American | 0.024% | 4,168 |
| Finnish (not grpmax-eligible) | 0.0223% | 4,494 |
| Ashkenazi Jewish (not grpmax-eligible) | 0.0135% | 7,385 |

*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.*

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2026-06-01.

**Submitter consensus:** conflicting (6 Likely benign, 1 Uncertain significance).

**Submission history:** 7 submissions (2018–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Illumina Laboratory Services, Illumina | Uncertain significance | criteria provided, single submitter | clinical testing | 2018-01-13 |
| GeneDx | Likely benign | criteria provided, single submitter | clinical testing | 2020-05-11 |
| PreventionGenetics, part of Exact Sciences | Likely benign | no assertion criteria provided | clinical testing | 2023-05-16 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2026-02-04 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-09-10 |
| Mayo Clinic Laboratories, Mayo Clinic | Likely benign | criteria provided, single submitter | clinical testing | 2025-03-25 |
| CeGaT Center for Human Genetics Tuebingen | Likely benign | criteria provided, single submitter | clinical testing | 2026-06-01 |

## Associated conditions {#conditions}

[glycogen storage disease due to phosphoglycerate mutase deficiency](https://sugi.bio/atlas/disease/glycogen-storage-disease-due-to-phosphoglycerate-mutase-deficiency/).

**Reported phenotype names (ClinVar):** Glycogen storage disease type X, not provided, PGAM2-related disorder, not specified, AllHighlyPenetrant, none provided, GSD X, MYOPATHY DUE TO PHOSPHOGLYCERATE MUTASE DEFICIENCY, PGAMM DEFICIENCY, PHOSPHOGLYCERATE MUTASE, MUSCLE, DEFICIENCY OF.

### 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 360272). 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.*