MCEE p.Val4=
c.12G>C · rs1572894873 · VCV759921
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.49e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.16 | GERP -1.3 |
| Overall | ||
| CADD | 5.498 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.49e-05%
European (non-Finnish) · 1/1,177,662 alleles
Overall
6.22e-05%
1/1,607,024 alleles · very rare
exomes 1/1,454,690 · genomes 0/152,334 · 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
- MCEE
- Protein
- p.Val4=
- Coding
- c.12G>C
- MANE Select
- NM_032601
- dbSNP
- rs1572894873
- Type
- single nucleotide variant
- Location
- chr2:71130208 (GRCh38)
- Gene constraint
- LOEUF 0.867 · pLI 0.41 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 87.27 · 2 PDB
Similar variants
- MCEE p.Val4Leu Uncertain significance ★ ⚠ same residue
- MCEE c.379-644A>G Likely pathogenic ★★ same type
- MCEE p.Arg47Ter Pathogenic ★★ same type
- MCEE p.Arg47Leu Uncertain significance ★★ ⚠ same type
- MCEE p.Asn115Lys Uncertain significance ★★ ⚠ same type
- MCEE p.Glu174Gln Uncertain significance ★★ same type
- MCEE p.Ile159Thr Uncertain significance ★★ ⚠ same type
- MCEE p.Leu79Val 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/mcee-p-val4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown