# NM_001382391.1(CSPP1):c.3157C>T (p.Pro1053Ser)

https://sugi.bio/variant/cspp1-p-pro1053ser

## Summary

**CSPP1 p.Pro1053Ser (c.3157C>T)** is classified **Uncertain significance** in CSPP1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-09-05). Ultra-rare (popmax 0.0167%, nfe); Associated with Inborn genetic diseases.

**At a glance:** Uncertain significance · review: Multiple submitters · rsID rs371681100 · 3 submitters · 2 linked conditions · ultra-rare (popmax 0.0167%, nfe)

## For patients & families {#patients}

This is a change in the CSPP1 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 3 submitters, and is linked to Inborn genetic diseases.

*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:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CSPP1](https://sugi.bio/atlas/gene/CSPP1/) |
| Protein change (HGVS p.) | p.Pro1053Ser |
| Coding change (HGVS c.) | c.3157C>T |
| MANE Select transcript | [NM_006421](https://www.ncbi.nlm.nih.gov/nuccore/NM_006421) (variant reported on NM_001382391) |
| dbSNP | [rs371681100](https://www.ncbi.nlm.nih.gov/snp/rs371681100/) |
| Variant type | single nucleotide variant |
| Location | chr8:67179863-67179863 (GRCh38) |
| ClinVar | [VCV861929](https://www.ncbi.nlm.nih.gov/clinvar/variation/861929/) |

**All HGVS expressions:** `NC_000008.10:g.68092098C>T`, `NC_000008.11:g.67179863C>T`, `NG_034100.1:g.120496C>T`, `NM_001291339.2:c.2107C>T`, `NM_001363131.2:c.3076C>T`, `NM_001363132.2:c.2962C>T`, `NM_001363133.2:c.2881C>T`, `NM_001364869.1:c.3223C>T`, `NM_001364870.1:c.3043C>T`, `NM_001382391.1:c.3157C>T`, `NM_001413186.1:c.5368-4291G>A`, `NM_001413187.1:c.5386-4291G>A`, `NM_001438330.1:c.2989C>T`, `NM_001438331.1:c.3142C>T`, `NM_001438332.1:c.2458C>T`, `NM_024790.7:c.3142C>T`

## 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 1.282, GERP -2.7, phastCons 0.971 — weakly conserved position
- CADD: **PHRED 14.86**. 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 0.96** across the covering region of the MANE Select transcript (67,074,253–67,195,590), spanning 121,337 bp. Chi-square p 0.15. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code 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 **0.0167%** (nfe) · FAF95 0.0148% · FAF99 0.014% · 194/1,159,882 in the highest group · 203/1,589,478 alleles overall — ultra-rare (popmax 0.0167%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| European (non-Finnish) (grpmax) | 0.0167% | 5,979 |
| Remaining individuals (not grpmax-eligible) | 0.00972% | 10,290 |
| Admixed American | 0.00168% | 59,480 |
| Finnish (not grpmax-eligible) | 0.00158% | 63,466 |
| African / African-American | 0.00135% | 74,340 |

*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}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2025-09-05.

**Submitter consensus:** unanimous (3/3 Uncertain significance).

**Submission history:** 3 submissions (2021–2025); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2021-06-18 |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-09-05 |
| Blueprint Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2024-10-21 |

## Associated conditions {#conditions}

[Inborn genetic diseases](https://sugi.bio/atlas/disease/inborn-genetic-diseases/), [Joubert syndrome 21](https://sugi.bio/atlas/disease/joubert-syndrome-21/).

**Reported phenotype names (ClinVar):** Inborn genetic diseases, Joubert syndrome 21, not provided, none provided.

### 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 861929). 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.*