MLPH p.Val570=
c.1710G>A · rs41270745 · VCV716627
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.495%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.046 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.41 | GERP 0.59, phastCons 0.019 |
| Overall | ||
| CADD | 6.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.495%
Middle Eastern · 30/6,062 alleles
Filtering AF
0.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.396%
Overall
0.339%
5,476/1,614,020 alleles · rare
exomes 5,179/1,461,800 · genomes 297/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.495% | 202 |
| European (non-Finnish) | 0.41% | 244 |
| Remaining individualsnot grpmax-eligible | 0.341% | 293 |
| South Asian | 0.194% | 515 |
| Ashkenazi Jewishnot grpmax-eligible | 0.172% | 580 |
| Finnishnot grpmax-eligible | 0.106% | 942 |
| African / African-American | 0.076% | 1,316 |
| Admixed American | 0.0717% | 1,396 |
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
- MLPH
- Protein
- p.Val570=
- Coding
- c.1710G>A
- MANE Select
- NM_024101
- dbSNP
- rs41270745
- Type
- single nucleotide variant
- Location
- chr2:237552371 (GRCh38)
- Gene constraint
- LOEUF 0.856 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 61.58
- Residue 570
- the 'disordered' region
Similar variants
- MLPH p.Arg35Gln Pathogenic/Likely pathogenic ★★ same type
- MLPH p.Arg35Trp Pathogenic/Likely pathogenic ★★ same type
- MLPH p.Ala236Thr Uncertain significance ★★ ⚠ same type
- MLPH p.Ala520Ser Uncertain significance ★★ ⚠ same type
- MLPH p.Arg375Cys Uncertain significance ★★ ⚠ same type
- MLPH p.Arg507Trp Uncertain significance ★★ ⚠ same type
- MLPH p.Arg518Gly Uncertain significance ★★ ⚠ same type
- MLPH p.Asp194Asn 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/mlph-p-val570 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown