UTRN p.Ser569Arg
c.1705A>C · VCV4603403
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.8629 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/2 damaging
AlphaMissense, REVEL · SaProt no call
Computational evidence
| Protein change | ||
| AlphaMissense | 0.8629 | likely pathogenic |
|---|---|---|
| REVEL | 0.153 | moderately benign-leaning |
| SaProt | — | not scored · why |
| ⇒ AlphaMissense calls this damaging; REVEL does not; SaProt makes no call. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 9.2 | GERP 2.1, phastCons 1 |
| Regional constraint | o/e 1.02 | unconstrained · MANE · 119 kb · p 0.35 · regional, not allelic |
| Overall | ||
| CADD | 24.2 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- UTRN
- Protein
- p.Ser569Arg
- Coding
- c.1705A>C
- MANE Select
- NM_007124
- Type
- single nucleotide variant
- Location
- chr6:144447301 (GRCh38)
- Gene constraint
- LOEUF 0.665 · pLI <0.01 (gnomAD)
- Residue 569
- the 'interaction with synm' region
Similar variants
- 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
- UTRN p.Thr2288= 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-ser569arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown