# NM_000308.4(CTSA):c.612G>A (p.Val204=)

https://sugi.bio/variant/ctsa-p-val204

## Summary

**CTSA p.Val204= (c.612G>A)** is classified **Likely benign** in CTSA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-22). Very rare (popmax 0.000169%, nfe); Associated with galactosialidosis.

**At a glance:** Likely benign · review: Single submitter · 1 submitter · 1 linked condition · very rare (popmax 0.000169%, nfe)

## For patients & families {#patients}

This is a change in the CTSA gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter, and is linked to galactosialidosis.

*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) | All ages |
| Clinical trials | 3 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | CTSA is a diagnostic-grade gene on 15 Genomics England panels |

**Commonly reported features of Galactosialidosis** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Coarse facial features — Very frequent (99-80%)
- Hearing impairment — Very frequent (99-80%)
- Abnormality of the vertebral column — Very frequent (99-80%)
- Intellectual disability — Very frequent (99-80%)
- Seizure — Very frequent (99-80%)
- Skeletal dysplasia — Very frequent (99-80%)
- Abnormal vertebral morphology — Very frequent (99-80%)
- Corneal opacity — Very frequent (99-80%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0003953/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CTSA](https://sugi.bio/atlas/gene/CTSA/) |
| Protein change (HGVS p.) | p.Val204= |
| Coding change (HGVS c.) | c.612G>A |
| MANE Select transcript | [NM_000308](https://www.ncbi.nlm.nih.gov/nuccore/NM_000308) |
| Variant type | single nucleotide variant |
| Location | chr20:45893231-45893231 (GRCh38) |
| ClinVar | [VCV4809391](https://www.ncbi.nlm.nih.gov/clinvar/variation/4809391/) |

**All HGVS expressions:** `NC_000020.10:g.44521870G>A`, `NC_000020.11:g.45893231G>A`, `NG_008291.1:g.7280G>A`, `NG_033108.1:g.3057C>T`, `NM_000308.4:c.612G>A`, `NM_001127695.3:c.612G>A`, `NM_001167594.3:c.561G>A`, `NR_133656.2:n.664G>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 3.46, GERP 0.602, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 15.48**. 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 **0.000169%** (nfe) · FAF95 2.8e-05% · FAF99 1.1e-05% · 2/1,179,972 in the highest group · 25/1,613,972 alleles overall — very rare (popmax 0.000169%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Finnish (not grpmax-eligible) | 0.0359% | 2,784 |
| European (non-Finnish) (grpmax) | 0.000169% | 589,984 |

Finnish shows a higher raw frequency than the grpmax group. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and "Remaining individuals" — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

*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}

**CTSA** population constraint: LOEUF 0.851, pLI 1.4137e-09, missense-Z 1.6492. *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):

- **galactosialidosis** — Definitive (AR)

## Protein context {#protein}

Residue **204** lies in a β-strand; a disulfide bond.

AlphaFold model confidence (whole protein): pLDDT 94.59, 87% of residues very-high.

**12 experimental structure(s)** (PDB): [1IVY](https://www.rcsb.org/structure/1IVY), [3BP4](https://www.rcsb.org/structure/3BP4), [3BP7](https://www.rcsb.org/structure/3BP7), [3BXN](https://www.rcsb.org/structure/3BXN), [4AZ0](https://www.rcsb.org/structure/4AZ0), [4AZ3](https://www.rcsb.org/structure/4AZ3).

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

*Describes the biological roles of CTSA (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:** CTSA's established molecular role includes carboxypeptidase activity. In Reactome, CTSA is annotated in disease pathway(s) including **Defective NEU1 causes sialidosis**.

**Disease mechanism (Reactome):** CTSA loss or alteration is curated in [Defective NEU1 causes sialidosis](https://reactome.org/content/detail/R-HSA-4341670).

### Pathways affected {#pathways}

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

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective NEU1 causes sialidosis](https://reactome.org/content/detail/R-HSA-4341670) | curated |
| [Glycosphingolipid catabolism](https://reactome.org/content/detail/R-HSA-9840310) | curated |
| [MHC class II antigen presentation](https://reactome.org/content/detail/R-HSA-2132295) | curated |
| [Neutrophil degranulation](https://reactome.org/content/detail/R-HSA-6798695) | curated |
| [Processing of antigen in germinal center B cells](https://reactome.org/content/detail/R-HSA-9979719) | curated |
| [Sialic acid metabolism](https://reactome.org/content/detail/R-HSA-4085001) | curated |

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

**Molecular function:** carboxypeptidase activity, serine-type carboxypeptidase activity.

**Biological process:** proteolysis, regulation of protein stability, negative regulation of chaperone-mediated autophagy.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-11-22.

**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 | 2025-11-22 |

## Associated conditions {#conditions}

[galactosialidosis](https://sugi.bio/atlas/disease/galactosialidosis/).

**Reported phenotype names (ClinVar):** Combined deficiency of sialidase AND beta galactosidase, Galactosialidosis, CATHEPSIN A DEFICIENCY, GOLDBERG SYNDROME, NEURAMINIDASE DEFICIENCY WITH BETA-GALACTOSIDASE DEFICIENCY, NEURAMINIDASE/BETA-GALACTOSIDASE EXPRESSION, PPCA DEFICIENCY, PROTECTIVE PROTEIN/CATHEPSIN A DEFICIENCY.

## Similar variants {#similar}

Related CTSA variant pages (same residue, condition, or type): [CTSA c.1-2A>G](/variant/ctsa-c-1-minus-2a-g), [CTSA c.358-2A>G](/variant/ctsa-c-358-minus-2a-g), [CTSA c.601-2A>G](/variant/ctsa-c-601-minus-2a-g), [CTSA c.692+3A>G](/variant/ctsa-c-692-plus-3a-g), [CTSA c.948+1G>A](/variant/ctsa-c-948-plus-1g-a), [CTSA p.Arg375Ter](/variant/ctsa-p-arg375ter), [CTSA p.Cys256Ter](/variant/ctsa-p-cys256ter), [CTSA p.Cys281Ter](/variant/ctsa-p-cys281ter).

### 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 4809391). 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.*