UGGT1 p.Asp92=
c.276C>T · rs149221713 · VCV2651345
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00716%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.38 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.69 | GERP 0.73, phastCons 0.01 |
| Overall | ||
| CADD | 13.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00716%
East Asian · 3/41,890 alleles
Filtering AF
0.0022%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00194%
Overall
0.00309%
48/1,553,050 alleles · very rare
exomes 46/1,401,020 · genomes 2/152,030 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00716% | 13,963 |
| South Asian | 0.00503% | 19,893 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00361% | 27,698 |
| Remaining individualsnot grpmax-eligible | 0.00335% | 29,859 |
| European (non-Finnish) | 0.00302% | 33,081 |
| Admixed American | 0.0022% | 45,360 |
| Finnishnot grpmax-eligible | 0.00159% | 62,698 |
| African / African-American | 0.0014% | 71,508 |
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
- UGGT1
- Protein
- p.Asp92=
- Coding
- c.276C>T
- MANE Select
- NM_020120
- dbSNP
- rs149221713
- Type
- single nucleotide variant
- Location
- chr2:128104013 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.97
Similar variants
- UGGT1 p.Glu918Lys Uncertain significance ★★ ⚠ same type
- UGGT1 p.Pro1126Leu Uncertain significance ★★ ⚠ same type
- UGGT1 c.278-9C>T Benign ★★ same type
- UGGT1 c.3025-4C>T Benign/Likely benign ★★ same type
- UGGT1 c.4643-8T>G Benign ★★ same type
- UGGT1 p.Ala669Val Benign ★★ same type
- UGGT1 p.Asn1139Ser Benign ★★ same type
- UGGT1 p.Glu422= Benign ★★ 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/uggt1-p-asp92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown