THOC2 p.Leu49=
c.147C>T · VCV4952673
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 | GERP -2.5, phastCons 1 |
| Overall | ||
| CADD | 5.637 | PHRED · no single calibrated threshold — expert panels disagree |
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
- THOC2
- Protein
- p.Leu49=
- Coding
- c.147C>T
- MANE Select
- NM_001081550
- Type
- single nucleotide variant
- Location
- chrX:123706933 (GRCh38)
- Structure
- AlphaFold pLDDT 72.83 · 4 PDB
- Residue 49
- the 'anchor domain; interaction with thoc5 and thoc7' region; an α-helix
Similar variants
- THOC2 p.Cys615Tyr Likely pathogenic ★★ same type
- THOC2 p.Thr696Ile Pathogenic/Likely pathogenic ★★ same type
- THOC2 p.Ala912Pro Uncertain significance ★★ ⚠ same type
- THOC2 p.Arg1307Trp Uncertain significance ★★ ⚠ same type
- THOC2 p.Arg1468Lys Uncertain significance ★★ ⚠ same type
- THOC2 p.Asn208Ser Uncertain significance ★★ ⚠ same type
- THOC2 p.Asn414Tyr Uncertain significance ★★ ⚠ same type
- THOC2 p.Asn666Ser 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/thoc2-p-leu49 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown