# NM_002778.4(PSAP):c.1452G>A (p.Ser484=)

https://sugi.bio/variant/psap-p-ser484

## Summary

**PSAP p.Ser484= (c.1452G>A)** is classified **Benign/Likely benign** in PSAP (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-02-03). Low-frequency (popmax 2.46%, afr); Associated with Krabbe disease due to saposin A deficiency.

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs114389264 · 6 submitters · 5 linked conditions · low-frequency (popmax 2.46%, afr)

## For patients & families {#patients}

This is a change in the PSAP gene that is classified as benign/likely benign — not considered disease-causing, submitted by 6 submitters, and is linked to Krabbe disease due to saposin A 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.*

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0010289/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PSAP](https://sugi.bio/atlas/gene/PSAP/) |
| Protein change (HGVS p.) | p.Ser484= |
| Coding change (HGVS c.) | c.1452G>A |
| MANE Select transcript | [NM_002778](https://www.ncbi.nlm.nih.gov/nuccore/NM_002778) |
| dbSNP | [rs114389264](https://www.ncbi.nlm.nih.gov/snp/rs114389264/) |
| Variant type | single nucleotide variant |
| Location | chr10:71818704-71818704 (GRCh38) |
| ClinVar | [VCV300509](https://www.ncbi.nlm.nih.gov/clinvar/variation/300509/) |

**All HGVS expressions:** `NC_000010.10:g.73578461C>T`, `NC_000010.11:g.71818704C>T`, `NG_009301.1:g.37622G>A`, `NM_001042465.3:c.1461G>A`, `NM_001042466.3:c.1458G>A`, `NM_002778.4:c.1452G>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 -1.097, GERP -3.4 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 3.248**. 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** — this absence is genuinely unknown. Where a position sits between the lowest and the highest record the release holds for its gene, an absent score is a result and we state it as one; this position falls outside them, or the gene has no scored position at all, so that test did not reach here. It may lie outside the scored MANE transcript scope, or it may have been scored with all four deltas below Δ0.2 just past the last surviving record. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **2.46%** (afr) · FAF95 2.36% · FAF99 2.33% · 1,842/74,950 in the highest group · 2,056/1,613,902 alleles overall — low-frequency (popmax 2.46%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 2.46% | 41 |
| Remaining individuals (not grpmax-eligible) | 0.134% | 744 |
| Admixed American | 0.095% | 1,053 |
| Middle Eastern | 0.0661% | 1,514 |
| South Asian | 0.0165% | 6,070 |
| European (non-Finnish) | 0.00458% | 21,851 |

*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}

**PSAP** population constraint: LOEUF 0.507, pLI 0.95247, missense-Z 0.73992. *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):

- **metachromatic leukodystrophy due to saposin B deficiency** — Definitive (AR)
- **Krabbe disease due to saposin A deficiency** — Moderate (AR)
- **Gaucher disease due to saposin C deficiency** — Definitive (AR)
- **combined PSAP deficiency** — Definitive (AR)

## Protein context {#protein}

Residue **484** lies in the saposin b-type 4 domain.

AlphaFold model confidence (whole protein): pLDDT 73.90, 17% of residues very-high.

**21 experimental structure(s)** (PDB): [1M12](https://www.rcsb.org/structure/1M12), [1N69](https://www.rcsb.org/structure/1N69), [1SN6](https://www.rcsb.org/structure/1SN6), [2DOB](https://www.rcsb.org/structure/2DOB), [2GTG](https://www.rcsb.org/structure/2GTG), [2QYP](https://www.rcsb.org/structure/2QYP) — incl. mutant structure 2R0R.

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

*Describes the biological roles of PSAP (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:** PSAP's established molecular role includes protease binding. p.Ser484= falls in the saposin b-type 4 domain.


### Pathways affected {#pathways}

PSAP participates in **5 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [G alpha (i) signalling events](https://reactome.org/content/detail/R-HSA-418594) | curated |
| [Glycosphingolipid catabolism](https://reactome.org/content/detail/R-HSA-9840310) | curated |
| [Neutrophil degranulation](https://reactome.org/content/detail/R-HSA-6798695) | curated |
| [Peptide ligand-binding receptors](https://reactome.org/content/detail/R-HSA-375276) | curated |
| [Platelet degranulation ](https://reactome.org/content/detail/R-HSA-114608) | curated |

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

**Molecular function:** protease binding, phospholipid binding, identical protein binding, protein homodimerization activity, scaffold protein binding, ganglioside GM1 binding.

**Biological process:** lysosomal transport, gene expression, ganglioside GM1 transport to membrane.

## Clinical significance {#significance}

**Benign/Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-02-03.

**Submitter consensus:** conflicting (8 Benign, 1 Likely benign).

**Submission history:** 9 submissions (2018–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Illumina Laboratory Services, Illumina | Benign | criteria provided, single submitter | clinical testing | 2018-01-13 |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-02-03 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-11-13 |
| Natera, Inc. | Benign | no assertion criteria provided | clinical testing | 2020-09-16 |
| GeneDx | Benign | criteria provided, single submitter | clinical testing | 2019-03-29 |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |

## Associated conditions {#conditions}

[Krabbe disease due to saposin A deficiency](https://sugi.bio/atlas/disease/krabbe-disease-due-to-saposin-a-deficiency/), [Krabbe disease](https://sugi.bio/atlas/disease/krabbe-disease/), [metachromatic leukodystrophy due to saposin B deficiency](https://sugi.bio/atlas/disease/metachromatic-leukodystrophy-due-to-saposin-b-deficiency/), [Gaucher disease due to saposin C deficiency](https://sugi.bio/atlas/disease/gaucher-disease-due-to-saposin-c-deficiency/), [combined PSAP deficiency](https://sugi.bio/atlas/disease/combined-psap-deficiency/).

**Reported phenotype names (ClinVar):** Krabbe disease due to saposin A deficiency, Gaucher disease due to saposin C deficiency, Combined PSAP deficiency, Sphingolipid activator protein 1 deficiency, Galactosylceramide beta-galactosidase deficiency, not provided, not specified, KRABBE DISEASE, ATYPICAL, DUE TO SAPOSIN A DEFICIENCY, Saposin A Deficiency, Encephalopathy due to prosaposin deficiency.

## Similar variants {#similar}

Related PSAP variant pages (same residue, condition, or type): [PSAP c.1005+1G>A](/variant/psap-c-1005-plus-1g-a), [PSAP c.375+1G>T](/variant/psap-c-375-plus-1g-t), [PSAP c.576+1G>A](/variant/psap-c-576-plus-1g-a), [PSAP c.577-1G>T](/variant/psap-c-577-minus-1g-t), [PSAP c.721-1G>A](/variant/psap-c-721-minus-1g-a), [PSAP p.Asn215His](/variant/psap-p-asn215his), [PSAP p.Asn215Lys](/variant/psap-p-asn215lys), [PSAP p.Cys241Ser](/variant/psap-p-cys241ser).

### 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 300509). 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.*