# NM_001368809.2(AMPD2):c.1587C>A (p.Thr529=)

https://sugi.bio/variant/ampd2-p-thr529

## Summary

**AMPD2 p.Thr529= (c.1587C>A)** is classified **Benign/Likely benign** in AMPD2 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-28). Rare (popmax 0.437%, afr); Associated with hereditary spastic paraplegia 63.

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs35337955 · 5 submitters · 2 linked conditions · rare (popmax 0.437%, afr)

## For patients & families {#patients}

This is a change in the AMPD2 gene that is classified as benign/likely benign — not considered disease-causing, submitted by 5 submitters, and is linked to hereditary spastic paraplegia 63.

*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 |
| Diagnostic panels | AMPD2 is a diagnostic-grade gene on 12 Genomics England panels |

**Commonly reported features of Autosomal recessive spastic paraplegia type 63** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Spasticity — Frequent (79-30%)
- Hypertonia — Frequent (79-30%)
- Hyperreflexia — Frequent (79-30%)
- Delayed gross motor development — Frequent (79-30%)
- Skeletal muscle atrophy — Frequent (79-30%)
- Short stature — Frequent (79-30%)
- Decreased body weight — Frequent (79-30%)
- Scissor gait — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0017658/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [AMPD2](https://sugi.bio/atlas/gene/AMPD2/) |
| Protein change (HGVS p.) | p.Thr529= |
| Coding change (HGVS c.) | c.1587C>A |
| MANE Select transcript | [NM_001368809](https://www.ncbi.nlm.nih.gov/nuccore/NM_001368809) |
| dbSNP | [rs35337955](https://www.ncbi.nlm.nih.gov/snp/rs35337955/) |
| Variant type | single nucleotide variant |
| Location | chr1:109629124-109629124 (GRCh38) |
| ClinVar | [VCV703122](https://www.ncbi.nlm.nih.gov/clinvar/variation/703122/) |

**All HGVS expressions:** `NC_000001.10:g.110171746C>A`, `NC_000001.11:g.109629124C>A`, `NG_034075.1:g.14312C>A`, `NG_082146.2:g.1585C>A`, `NM_001257360.1:c.1749C>A`, `NM_001257361.2:c.1395C>A`, `NM_001308170.1:c.1524C>A`, `NM_001368809.2:c.1587C>A`, `NM_004037.9:c.1587C>A`, `NM_139156.4:c.1506C>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 -0.33, GERP -3.83, phastCons 0.089 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 13.67**. 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 **0.437%** (afr) · FAF95 0.398% · FAF99 0.383% · 328/75,048 in the highest group · 371/1,613,902 alleles overall — rare (popmax 0.437%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 0.437% | 229 |
| Remaining individuals (not grpmax-eligible) | 0.0544% | 1,838 |
| Admixed American | 0.0117% | 8,572 |
| European (non-Finnish) | 0.000169% | 589,977 |

*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}

**AMPD2** population constraint: LOEUF 0.705, pLI 1.3901e-08, missense-Z 3.6393. *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 **529** lies in an α-helix.

AlphaFold model confidence (whole protein): pLDDT 81.28, 59% of residues very-high.

**5 experimental structure(s)** (PDB): [26XC](https://www.rcsb.org/structure/26XC), [4NO3](https://www.rcsb.org/structure/4NO3), [4NO5](https://www.rcsb.org/structure/4NO5), [8HU6](https://www.rcsb.org/structure/8HU6), [8HUB](https://www.rcsb.org/structure/8HUB).

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

*Describes the biological roles of AMPD2 (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:** AMPD2's established molecular role includes AMP deaminase activity.


### Pathways affected {#pathways}

AMPD2 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Purine salvage](https://reactome.org/content/detail/R-HSA-74217) | curated |

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

**Molecular function:** AMP deaminase activity, identical protein binding.

**Biological process:** IMP biosynthetic process, GMP salvage, cyclic purine nucleotide metabolic process, energy homeostasis.

## Clinical significance {#significance}

**Benign/Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-01-28.

**Submitter consensus:** conflicting (5 Likely benign, 1 Benign).

**Submission history:** 6 submissions (2019–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Likely benign | criteria provided, single submitter | clinical testing | 2021-03-17 |
| Genome-Nilou Lab | Likely benign | criteria provided, single submitter | clinical testing | 2023-04-11 |
| Breakthrough Genomics, Breakthrough Genomics | Likely benign | criteria provided, single submitter | not provided |  |
| PreventionGenetics, part of Exact Sciences | Likely benign | no assertion criteria provided | clinical testing | 2019-11-07 |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-01-28 |

## Associated conditions {#conditions}

[hereditary spastic paraplegia 63](https://sugi.bio/atlas/disease/hereditary-spastic-paraplegia-63/), [pontocerebellar hypoplasia type 9](https://sugi.bio/atlas/disease/pontocerebellar-hypoplasia-type-9/).

**Reported phenotype names (ClinVar):** Hereditary spastic paraplegia 63, Pontocerebellar hypoplasia type 9, not provided, AMPD2-related disorder, AMPD2-related condition, Spastic paraplegia 63, autosomal recessive, none provided.

## Similar variants {#similar}

Related AMPD2 variant pages (same residue, condition, or type): [AMPD2 c.1698+1G>A](/variant/ampd2-c-1698-plus-1g-a), [AMPD2 p.Arg353Ter](/variant/ampd2-p-arg353ter), [AMPD2 p.Arg449Ter](/variant/ampd2-p-arg449ter), [AMPD2 p.Arg620His](/variant/ampd2-p-arg620his), [AMPD2 p.Arg789His](/variant/ampd2-p-arg789his), [AMPD2 p.Glu174Ter](/variant/ampd2-p-glu174ter), [AMPD2 c.1080+3G>A](/variant/ampd2-c-1080-plus-3g-a), [AMPD2 c.353+3G>A](/variant/ampd2-c-353-plus-3g-a).

### 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 703122). 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.*