CSDE1 p.Asn149=
c.447C>T · VCV4821559
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0231%, sas)
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 -1.8 | GERP -4.7 |
| Overall | ||
| CADD | 0.927 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0231%
South Asian · 21/90,964 alleles
Filtering AF
0.0154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0129%
Overall
0.00254%
41/1,612,734 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0231% | 4,332 |
| East Asian | 0.0111% | 8,972 |
| Admixed American | 0.00834% | 11,996 |
| African / African-American | 0.00267% | 37,428 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,402 |
| European (non-Finnish) | 0.000594% | 168,483 |
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.Asn149=
- Coding
- c.447C>T
- MANE Select
- NM_001007553
- Type
- single nucleotide variant
- Location
- chr1:114736811 (GRCh38)
- Gene constraint
- LOEUF 0.295 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.05 · 5 PDB
- Residue 149
- the csd 2; truncated 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.Phe699= Benign/Likely benign ★★ same type
- CSDE1 p.Ser75= Benign ★★ same type
- CSDE1 c.500+1G>C 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-asn149 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown