RNMT p.Glu460=
c.1380A>G · rs1598428300 · VCV757966
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00112%, sas)
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 2.6 | GERP 0.33, phastCons 1 |
| Overall | ||
| CADD | 10.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00112%
South Asian · 1/89,514 alleles
Filtering AF
2.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000212%
3/1,412,180 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00112% | 89,514 |
| European (non-Finnish) | 0.000176% | 568,282 |
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
- RNMT
- Protein
- p.Glu460=
- Coding
- c.1380A>G
- MANE Select
- NM_003799
- dbSNP
- rs1598428300
- Type
- single nucleotide variant
- Location
- chr18:13754134 (GRCh38)
- Gene constraint
- LOEUF 0.92 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.27 · 8 PDB
- Residue 460
- the mrna cap 0 methyltransferase domain; an α-helix
Similar variants
- RNMT p.Glu460Asp Uncertain significance ★ ⚠ same residue
- RNMT p.Tyr399= Benign ★★ same type
- RNMT p.Ala151Val Uncertain significance ★ ⚠ same type
- RNMT p.Ala2Thr Uncertain significance ★ ⚠ same type
- RNMT p.Ala56Thr Uncertain significance ★ ⚠ same type
- RNMT p.Arg107Gly Uncertain significance ★ ⚠ same type
- RNMT p.Arg239Trp Uncertain significance ★ ⚠ same type
- RNMT p.Arg247Cys Uncertain significance ★ ⚠ 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/rnmt-p-glu460 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown