TFE3 p.Ser158=
c.474T>G · rs782341363 · VCV2660504
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0046%, nfe)
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 0.25 | GERP -0.36 |
| Overall | ||
| CADD | 7.811 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0046%
European (non-Finnish) · 41/890,361 alleles
Filtering AF
0.00343%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00308%
Overall
0.00341%
41/1,201,233 alleles · very rare
exomes 37/1,090,488 · genomes 4/110,745 · joint denominator
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
- TFE3
- Protein
- p.Ser158=
- Coding
- c.474T>G
- MANE Select
- NM_006521
- dbSNP
- rs782341363
- Type
- single nucleotide variant
- Location
- chrX:49039167 (GRCh38)
- Structure
- AlphaFold pLDDT 60.54 · 1 PDB
Similar variants
- TFE3 p.Arg117Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- TFE3 p.Thr187Met Pathogenic/Likely pathogenic ★★ same type
- TFE3 p.Gly370Ser Uncertain significance ★★ ⚠ same type
- TFE3 p.His509Asn Uncertain significance ★★ ⚠ same type
- TFE3 p.Pro495Ser Uncertain significance ★★ ⚠ same type
- TFE3 p.Ser153Pro Uncertain significance ★★ ⚠ same type
- TFE3 p.Ser377Asn Uncertain significance ★★ ⚠ same type
- TFE3 p.Val311Met 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/tfe3-p-ser158 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown