CSDE1 p.Phe699=
c.2097T>C · rs72994458 · VCV730389
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.26%, 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 6.2 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 12.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.26%
African / African-American · 942/75,036 alleles
Filtering AF
1.19%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.16%
Overall
0.0616%
995/1,614,138 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.26% | 80 |
| Remaining individualsnot grpmax-eligible | 0.048% | 2,084 |
| Admixed American | 0.025% | 4,001 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.00549% | 18,214 |
| European (non-Finnish) | 0.000169% | 590,005 |
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.Phe699=
- Coding
- c.2097T>C
- MANE Select
- NM_001007553
- dbSNP
- rs72994458
- Type
- single nucleotide variant
- Location
- chr1:114719698 (GRCh38)
- Gene constraint
- LOEUF 0.295 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.05 · 5 PDB
- Residue 699
- a β-strand; the csd 9 domain
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.Ser75= 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-phe699 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown