CSPP1 p.Arg877His
c.2630G>A · rs16933182 · VCV379388
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 31%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
Joubert syndrome 21
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.024 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.6 | GERP -1.6, phastCons 1 |
| Regional constraint | o/e 0.96 | unconstrained · MANE · 121 kb · p 0.15 · regional, not allelic |
| Overall | ||
| CADD | 20.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
31%
African / African-American · 23,061/74,440 alleles
Filtering AF
30.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 30.5%
Overall
5.3%
84,948/1,601,592 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 31% | 3 |
| Finnishnot grpmax-eligible | 11.4% | 9 |
| Admixed American | 8.67% | 12 |
| South Asian | 8.35% | 12 |
| Remaining individualsnot grpmax-eligible | 5.94% | 17 |
| Middle Eastern | 4.73% | 21 |
| Ashkenazi Jewishnot grpmax-eligible | 4.46% | 22 |
| East Asian | 3.34% | 30 |
| European (non-Finnish) | 3% | 33 |
| Amishnot grpmax-eligible | 1.54% | 65 |
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.Arg877His
- Coding
- c.2630G>A
- MANE Select
- NM_001382391
- dbSNP
- rs16933182
- Type
- single nucleotide variant
- Location
- chr8:67161902 (GRCh38)
- Gene constraint
- LOEUF 0.876 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 57.34
Similar variants
- CSPP1 p.Arg877Cys Uncertain significance ★★ same residue
- CSPP1 p.Arg877= Likely benign ★★ same residue
- CSPP1 c.1022+1G>T Likely pathogenic ★★ same condition
- CSPP1 c.1187+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CSPP1 c.1497-2A>C Likely pathogenic ★★ same condition
- CSPP1 c.1697+1G>T Pathogenic/Likely pathogenic ★★ same condition
- CSPP1 c.2968+1G>A Pathogenic ★★ same condition
- CSPP1 c.2968+1G>T Pathogenic ★★ same condition
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-arg877his (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown