MID1 p.Arg540fs
c.1619_1638del · rs2518968722 · VCV992858
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 | escapes | premature termination codon within the last 50 nt of the penultimate exon (9 of 10, 17 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 6.1 | GERP 1.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- MID1
- Protein
- p.Arg540fs
- Coding
- c.1619_1638del
- MANE Select
- NM_000381
- dbSNP
- rs2518968722
- Type
- Deletion
- Location
- chrX:10454887 (GRCh38)
- Structure
- AlphaFold pLDDT 86.51 · 5 PDB
- Residue 540
- the b30.2/spry domain; a β-strand
Similar variants
- MID1 p.Arg540Gln Uncertain significance ★ ⚠ same residue
- MID1 c.661-7del Benign/Likely benign ★★ same type
- MID1 c.661-8_661-7del Benign/Likely benign ★★ same type
- MID1 p.Ala127fs Likely pathogenic ★ same type
- MID1 p.Arg308fs Likely pathogenic ★ same type
- MID1 p.Asp129fs Likely pathogenic ★ same type
- MID1 p.Cys392fs Likely pathogenic ★ same type
- MID1 p.Glu317fs Pathogenic ★ 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/mid1-p-arg540fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown