INMT p.Phe113=
c.339C>T · rs116690173 · VCV722841
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.09%, afr)
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 -6.7 | GERP -3.4 |
| Overall | ||
| CADD | 6.225 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.09%
African / African-American · 1,566/75,008 alleles
Filtering AF
2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.97%
Overall
0.118%
1,901/1,613,992 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.09% | 48 |
| Middle Eastern | 0.251% | 398 |
| Remaining individualsnot grpmax-eligible | 0.189% | 530 |
| Admixed American | 0.188% | 531 |
| European (non-Finnish) | 0.00703% | 14,217 |
| South Asian | 0.00659% | 15,176 |
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
- INMT
- Protein
- p.Phe113=
- Coding
- c.339C>T
- MANE Select
- NM_006774
- dbSNP
- rs116690173
- Type
- single nucleotide variant
- Location
- chr7:30753915 (GRCh38)
- Gene constraint
- LOEUF 1.467 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.14 · 1 PDB
- Residue 113
- an α-helix
Similar variants
- INMT c.363-7T>A Likely benign ★★ same type
- INMT p.Ala104Thr Uncertain significance ★ ⚠ same type
- INMT p.Ala134Glu Uncertain significance ★ ⚠ same type
- INMT p.Ala215Thr Uncertain significance ★ ⚠ same type
- INMT p.Ala247Ser Uncertain significance ★ ⚠ same type
- INMT p.Ala247Val Uncertain significance ★ ⚠ same type
- INMT p.Arg137Trp Uncertain significance ★ ⚠ same type
- INMT p.Arg177His 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/inmt-p-phe113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown