MITF p.Leu244Pro
c.730_731delinsCC · rs1553702406 · VCV547530
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
1
Waardenburg syndrome type 2A
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.79 | GERP 2.1, phastCons 0.98 |
| Regional constraint | o/e 0.96 | unconstrained · MANE · 14 kb · p 0.51 · regional, not allelic |
Population frequency
dbSNP / gnomAD
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
- MITF
- Protein
- p.Leu244Pro
- Coding
- c.730_731delinsCC
- MANE Select
- NM_001354604
- dbSNP
- rs1553702406
- Type
- Indel
- Location
- chr3:69941299 (GRCh38)
- Gene constraint
- LOEUF 0.482 · pLI 0.99 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.25 · 12 PDB
- Residue 244
- the 'transactivation' region
Similar variants
- MITF p.Leu244Phe Uncertain significance ★★ ⚠ same residue
- MITF p.Leu244Ser Uncertain significance ★ same residue
- MITF p.Leu244= Likely benign ★ same residue
- MITF c.1031+1G>A Pathogenic ★★ same condition
- MITF c.1179+1G>A Pathogenic ★★ same condition
- MITF c.355-1062G>C Pathogenic/Likely pathogenic ★★ same condition
- MITF c.880+1G>A Likely pathogenic ★★ same condition
- MITF c.955+1G>A 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/mitf-p-leu244pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown