MID1 p.Ser538Ter
c.1608_1611dup · rs1556003095 · VCV547525
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | 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, 43 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 7.8 | 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.Ser538Ter
- Coding
- c.1608_1611dup
- MANE Select
- NM_000381
- dbSNP
- rs1556003095
- Type
- Duplication
- Location
- chrX:10454913 (GRCh38)
- Structure
- AlphaFold pLDDT 86.51 · 5 PDB
- Residue 538
- the b30.2/spry domain; a β-strand
Similar variants
- MID1 p.Ser483fs Pathogenic ★★ same condition
- MID1 p.Ser538Thr Benign/Likely benign ★★ same residue
- MID1 p.Lys564fs Likely pathogenic ★ same condition
- MID1 p.Tyr627Ter Likely pathogenic ★ same condition
- MID1 p.His541_Tyr542insLeuPheIleAspSerGlyArgHis Uncertain significance ★ same condition
- MID1 p.Glu520fs Pathogenic same condition
- MID1 p.Val440fs Pathogenic same condition
- MID1 p.Asp537_Ser538insAsp Uncertain significance 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-ser538ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown