MID1 p.Phe421fs
c.1259dup · VCV4948799
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
MID1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 7 of 10 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.35 | GERP -3.4, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- MID1
- Protein
- p.Phe421fs
- Coding
- c.1259dup
- MANE Select
- NM_000381
- Type
- Duplication
- Location
- chrX:10469722 (GRCh38)
- Structure
- AlphaFold pLDDT 86.51 · 5 PDB
- Residue 421
- the fibronectin type-iii domain
Disease context
MID1-related disorder
Similar variants
- MID1 p.Ile536delinsProArgArgValThrHisLeuAsnAlaSerProAlaArgGlyAlaMetGluTer Likely pathogenic ★ same condition
- MID1 p.Gln454Ter Likely pathogenic ★ same condition
- MID1 p.Ala34Asp Uncertain significance ★ ⚠ same condition
- MID1 p.Asp191Asn Uncertain significance ★ ⚠ same condition
- MID1 c.757-10784C>T Uncertain significance same condition
- MID1 c.757-5727G>A Uncertain significance same condition
- MID1 p.Leu292Pro Uncertain significance ⚠ same condition
- MID1 c.757-10802C>T Likely benign 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/mid1-p-phe421fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown