UTRN p.Arg2539=
c.7617A>G · rs142932212 · VCV713896
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0827%, mid)
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 1.2 | GERP -4.3, phastCons 1 |
| Overall | ||
| CADD | 11.51 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0827%
Middle Eastern · 5/6,046 alleles
Filtering AF
0.0739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0722%
Overall
0.0643%
1,036/1,612,254 alleles · ultra-rare
exomes 952/1,459,956 · genomes 84/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0827% | 1,209 |
| European (non-Finnish) | 0.0781% | 1,280 |
| Admixed American | 0.0685% | 1,460 |
| Remaining individualsnot grpmax-eligible | 0.0577% | 1,733 |
| South Asian | 0.022% | 4,544 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0203% | 4,923 |
| African / African-American | 0.008% | 12,499 |
| East Asian | 0.00223% | 44,786 |
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.Arg2539=
- Coding
- c.7617A>G
- MANE Select
- NM_007124
- dbSNP
- rs142932212
- Type
- single nucleotide variant
- Location
- chr6:144678543 (GRCh38)
- Gene constraint
- LOEUF 0.665 · pLI <0.01 (gnomAD)
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-arg2539 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown