UTRN p.Ala3393=
c.10179G>A · rs141979832 · VCV738473
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.141%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.93 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.72 | gain · loss 0.11 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -4.5 |
| Overall | ||
| CADD | 10.34 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.141%
South Asian · 128/91,060 alleles
Filtering AF
0.121%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.113%
Overall
0.0128%
206/1,613,646 alleles · rare
exomes 185/1,461,536 · genomes 21/152,110 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.141% | 711 |
| Middle Eastern | 0.0493% | 2,027 |
| African / African-American | 0.032% | 3,121 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,206 |
| Admixed American | 0.00333% | 29,993 |
| European (non-Finnish) | 0.00314% | 31,889 |
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
- UTRN
- Protein
- p.Ala3393=
- Coding
- c.10179G>A
- MANE Select
- NM_007124
- dbSNP
- rs141979832
- Type
- single nucleotide variant
- Location
- chr6:144840741 (GRCh38)
- Gene constraint
- LOEUF 0.665 · pLI <0.01 (gnomAD)
Similar variants
- UTRN p.Ala3393Val Uncertain significance ★ ⚠ same residue
- UTRN c.4437+9T>C Benign/Likely benign ★★ same type
- UTRN c.4594-8C>T Benign/Likely benign ★★ same type
- UTRN p.Arg1625Lys Likely benign ★★ same type
- UTRN p.Arg1967Trp Benign/Likely benign ★★ same type
- UTRN p.Gly1862Glu Likely benign ★★ same type
- UTRN p.Ile2227Val Likely benign ★★ same type
- UTRN p.Ser1561Cys 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/utrn-p-ala3393 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown