MTTP p.Lys522del
c.1562AGA[1] · rs1301806588 · VCV2096011
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
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 7.7 | GERP 1.6, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,026 alleles
Overall
6.2e-05%
1/1,613,274 alleles · very rare
exomes 1/1,460,960 · genomes 0/152,314 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- MTTP
- Protein
- p.Lys522del
- Coding
- c.1562AGA[1]
- MANE Select
- NM_001386140
- dbSNP
- rs1301806588
- Type
- Microsatellite
- Location
- chr4:99608768 (GRCh38)
- Gene constraint
- LOEUF 0.672 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.73 · 2 PDB
- Residue 522
- the vitellogenin domain; an α-helix
Similar variants
- MTTP p.Lys522Glu Uncertain significance ★★ ⚠ same residue
- MTTP p.His236fs Pathogenic ★★ same type
- MTTP c.1769+20TC[2] Likely benign ★★ same type
- MTTP c.502-12CTTT[3] Likely benign ★★ same type
- MTTP p.Leu435fs Pathogenic ★ same type
- MTTP p.Val539fs Pathogenic ★ same type
- MTTP p.Val92fs Likely pathogenic ★ same type
- MTTP p.Leu44del Uncertain significance ★ 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/mttp-p-lys522del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown