MAP7 p.Ser531Pro
c.1591T>C · VCV4103630
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.773 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
2/3 damaging
AlphaMissense, REVEL, SaProt
Computational evidence
| Protein change | ||
| AlphaMissense | 0.773 | likely pathogenic |
|---|---|---|
| REVEL | 0.057 | moderately benign-leaning |
| SaProt | LLR -10.50 | damaging |
| ⇒ AlphaMissense and SaProt call this damaging; REVEL does not. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -8 |
| Regional constraint | o/e 0.97 | unconstrained · MANE · 206 kb · p 0.43 · regional, not allelic |
| Overall | ||
| CADD | 9.392 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- MAP7
- Protein
- p.Ser531Pro
- Coding
- c.1591T>C
- MANE Select
- NM_003980
- Type
- single nucleotide variant
- Location
- chr6:136361115 (GRCh38)
- Gene constraint
- LOEUF 0.749 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.72 · 1 PDB
- Residue 531
- the 'disordered' region
Similar variants
- MAP7 p.Arg214Cys Uncertain significance ★★ ⚠ same type
- MAP7 c.1274-1G>C Uncertain significance ★ same type
- MAP7 c.67+24403G>A Uncertain significance ★ same type
- MAP7 c.67+24406A>G Uncertain significance ★ same type
- MAP7 c.67+24434G>T Uncertain significance ★ same type
- MAP7 c.752-21T>C Uncertain significance ★ same type
- MAP7 c.752-6G>A Uncertain significance ★ same type
- MAP7 p.Ala17Val 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/map7-p-ser531pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown