CSGALNACT1 p.Pro487=
c.1461C>T · rs553914582 · VCV2064311
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0538%, 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 -8 | GERP -4.7 |
| Overall | ||
| CADD | 0.409 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0538%
South Asian · 49/91,072 alleles
Filtering AF
0.0418%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0375%
Overall
0.00694%
112/1,614,110 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0538% | 1,859 |
| Middle Eastern | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,945 |
| Admixed American | 0.0117% | 8,574 |
| East Asian | 0.0111% | 8,973 |
| European (non-Finnish) | 0.00339% | 29,500 |
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
- CSGALNACT1
- Protein
- p.Pro487=
- Coding
- c.1461C>T
- MANE Select
- NM_001354483
- dbSNP
- rs553914582
- Type
- single nucleotide variant
- Location
- chr8:19405918 (GRCh38)
- Gene constraint
- LOEUF 1.257 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.71
Similar variants
- CSGALNACT1 p.Pro487Ala Uncertain significance ★ ⚠ same residue
- CSGALNACT1 p.Asn264Ser Likely pathogenic ★★ ⚠ same type
- CSGALNACT1 c.634+5G>C Uncertain significance ★★ same type
- CSGALNACT1 p.Ala195Ser Uncertain significance ★★ ⚠ same type
- CSGALNACT1 p.Ala259Gly Uncertain significance ★★ ⚠ same type
- CSGALNACT1 p.Ala401Ser Uncertain significance ★★ ⚠ same type
- CSGALNACT1 p.Ala48Gly Uncertain significance ★★ ⚠ same type
- CSGALNACT1 p.Arg202Cys Uncertain significance ★★ ⚠ 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/csgalnact1-p-pro487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown