CSDE1 p.Ser75=
c.225G>A · rs144707101 · VCV788636
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.08%, afr)
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 8 | GERP 0.33, phastCons 1 |
| Overall | ||
| CADD | 13.81 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.08%
African / African-American · 810/75,002 alleles
Filtering AF
1.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.994%
Overall
0.0547%
882/1,613,626 alleles · low-frequency
exomes 417/1,461,430 · genomes 465/152,196 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.08% | 93 |
| Admixed American | 0.0467% | 2,143 |
| Remaining individualsnot grpmax-eligible | 0.0448% | 2,231 |
| South Asian | 0.00769% | 13,007 |
| European (non-Finnish) | 0.000763% | 131,071 |
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
- CSDE1
- Protein
- p.Ser75=
- Coding
- c.225G>A
- MANE Select
- NM_001007553
- dbSNP
- rs144707101
- Type
- single nucleotide variant
- Location
- chr1:114738047 (GRCh38)
- Gene constraint
- LOEUF 0.295 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.05 · 5 PDB
- Residue 75
- the csd 1 domain; a β-strand
Similar variants
- CSDE1 p.Ala765Thr Uncertain significance ★★ ⚠ same type
- CSDE1 p.Arg132His Uncertain significance ★★ ⚠ same type
- CSDE1 p.Glu335Gly Uncertain significance ★★ same type
- CSDE1 c.2053-4T>C Benign/Likely benign ★★ same type
- CSDE1 c.2350-5C>A Benign/Likely benign ★★ same type
- CSDE1 p.Phe699= Benign/Likely benign ★★ same type
- CSDE1 c.500+1G>C Pathogenic ★ same type
- CSDE1 p.Arg348Ter Likely 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/csde1-p-ser75 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown