MARVELD2 p.Pro52=
c.156A>T · rs138816138 · VCV227542
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.084%, afr)
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 -6.4 | GERP -5.2 |
| Overall | ||
| CADD | 0.672 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.084%
African / African-American · 63/75,030 alleles
Filtering AF
0.0674%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0613%
Overall
0.00502%
81/1,614,118 alleles · ultra-rare
exomes 39/1,461,882 · genomes 42/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.084% | 1,191 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,946 |
| Admixed American | 0.0133% | 7,501 |
| South Asian | 0.0011% | 91,064 |
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
- MARVELD2
- Protein
- p.Pro52=
- Coding
- c.156A>T
- MANE Select
- NM_001038603
- dbSNP
- rs138816138
- Type
- single nucleotide variant
- Location
- chr5:69419541 (GRCh38)
- Gene constraint
- LOEUF 0.993 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 66.90 · 3 PDB
- Residue 52
- the 'disordered' region
Similar variants
- MARVELD2 c.1183-1G>A Pathogenic/Likely pathogenic ★★ same type
- MARVELD2 c.1331+1G>A Pathogenic ★★ same type
- MARVELD2 c.1331+2T>C Pathogenic/Likely pathogenic ★★ same type
- MARVELD2 p.Arg164Ter Likely pathogenic ★★ same type
- MARVELD2 p.Arg317Ter Pathogenic/Likely pathogenic ★★ same type
- MARVELD2 p.Arg455Ter Likely pathogenic ★★ same type
- MARVELD2 p.Arg500Ter Pathogenic/Likely pathogenic ★★ same type
- MARVELD2 p.Ser63Ter Likely pathogenic ★★ 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/marveld2-p-pro52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown