CSGALNACT1 p.Asp39=
c.117C>T · rs758278533 · VCV1649510
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00801%, 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 -0.6 | GERP -3.1 |
| Overall | ||
| CADD | 3.508 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,936 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00233%
Overall
0.00322%
52/1,614,024 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00801% | 12,489 |
| European (non-Finnish) | 0.00347% | 28,782 |
| Admixed American | 0.00333% | 30,002 |
| East Asian | 0.00223% | 44,882 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,486 |
| South Asian | 0.0011% | 91,088 |
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.Asp39=
- Coding
- c.117C>T
- MANE Select
- NM_001354483
- dbSNP
- rs758278533
- Type
- single nucleotide variant
- Location
- chr8:19505718 (GRCh38)
- Gene constraint
- LOEUF 1.257 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.71
Similar variants
- CSGALNACT1 p.Asp39Glu Uncertain significance ★★ ⚠ same residue
- CSGALNACT1 p.Asp39His 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
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-asp39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown