CSPP1 p.Asn243=
c.729C>T · VCV4900717
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.49 | GERP -3.5, phastCons 0.21 |
| Overall | ||
| CADD | 2.927 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,834 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000274%
4/1,461,716 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,834 |
| European (non-Finnish) | 0.000254% | 393,306 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CSPP1
- Protein
- p.Asn243=
- Coding
- c.729C>T
- MANE Select
- NM_001382391
- Type
- single nucleotide variant
- Location
- chr8:67095538 (GRCh38)
- Gene constraint
- LOEUF 0.876 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 57.34
- Residue 243
- the 'disordered' region
Similar variants
- CSPP1 p.Asn243Lys Uncertain significance ★★ same residue
- CSPP1 p.Asn243His Uncertain significance ★ same residue
- CSPP1 c.1022+1G>T Likely pathogenic ★★ same type
- CSPP1 c.1187+1G>A Pathogenic/Likely pathogenic ★★ same type
- CSPP1 c.1497-2A>C Likely pathogenic ★★ same type
- CSPP1 c.1697+1G>T Pathogenic/Likely pathogenic ★★ same type
- CSPP1 c.2968+1G>A Pathogenic ★★ same type
- CSPP1 c.2968+1G>T Pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cspp1-p-asn243 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown