UFM1 p.Pro17=
c.51G>A · rs143474592 · VCV3024786
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00415%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.048 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -8 | GERP -3.5 |
| Overall | ||
| CADD | 5.741 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00415%
European (non-Finnish) · 49/1,180,052 alleles
Filtering AF
0.00318%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00286%
Overall
0.00322%
52/1,614,108 alleles · very rare
exomes 46/1,461,894 · genomes 6/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00415% | 24,083 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
| African / African-American | 0.00133% | 74,936 |
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
- UFM1
- Protein
- p.Pro17=
- Coding
- c.51G>A
- MANE Select
- NM_016617
- dbSNP
- rs143474592
- Type
- single nucleotide variant
- Location
- chr13:38350047 (GRCh38)
- Gene constraint
- LOEUF 0.85 · pLI 0.62 (gnomAD)
- Structure
- AlphaFold pLDDT 91.84 · 14 PDB
Similar variants
- UFM1 p.Pro17Leu Likely benign same residue
- UFM1 p.Arg81Cys Likely pathogenic ★★ same type
- UFM1 p.Arg75Trp Uncertain significance ★★ ⚠ same type
- UFM1 p.Gly54Glu Uncertain significance ★★ ⚠ same type
- UFM1 p.Ser47Asn Uncertain significance ★★ ⚠ same type
- UFM1 c.118-20T>A Benign/Likely benign ★★ same type
- UFM1 c.2+25A>T Benign ★★ same type
- UFM1 c.59+104C>T Likely 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/ufm1-p-pro17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown