MED12 p.Phe2016=
c.6048T>C · rs2519720092 · VCV2704972
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
FG syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.191 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.3 | GERP 0.65, phastCons 1 |
| Overall | ||
| CADD | 10.42 | 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
- MED12
- Protein
- p.Phe2016=
- Coding
- c.6048T>C
- MANE Select
- NM_005120
- dbSNP
- rs2519720092
- Type
- single nucleotide variant
- Location
- chrX:71140638 (GRCh38)
- Structure
- AlphaFold pLDDT 65.80 · 3 PDB
- Residue 2016
- a UniProt-annotated variant site (in hdkr); the 'interaction with ctnnb1 and gli3' region
Similar variants
- MED12 p.Phe2016Leu Likely benign ★ ⚠ same residue
- MED12 p.Phe2016Cys Uncertain significance ★ ⚠ same residue
- MED12 c.6408+1G>A Pathogenic/Likely pathogenic ★★ same condition
- MED12 p.Arg1295Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- MED12 p.Arg1295His Pathogenic ★★ same condition
- MED12 p.Arg1357His Pathogenic/Likely pathogenic ★★ ⚠ same condition
- MED12 p.Arg296Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- MED12 p.Arg961Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
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/med12-p-phe2016 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown