MLNR p.Ser327=
c.981G>A · rs200619940 · VCV2643815
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.78%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.097 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.63 | GERP -3.8 |
| Overall | ||
| CADD | 5.776 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.78%
South Asian · 710/91,072 alleles
Filtering AF
0.732%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.713%
Overall
0.0489%
789/1,614,032 alleles · rare
exomes 752/1,461,878 · genomes 37/152,154 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.78% | 128 |
| Middle Eastern | 0.181% | 551 |
| Remaining individualsnot grpmax-eligible | 0.0512% | 1,953 |
| East Asian | 0.00668% | 14,961 |
| African / African-American | 0.00267% | 37,486 |
| European (non-Finnish) | 0.00254% | 39,334 |
| Admixed American | 0.00167% | 60,012 |
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
- MLNR
- Protein
- p.Ser327=
- Coding
- c.981G>A
- MANE Select
- NM_001507
- dbSNP
- rs200619940
- Type
- single nucleotide variant
- Location
- chr13:49222119 (GRCh38)
- Gene constraint
- LOEUF 1.484 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.99 · 4 PDB
- Residue 327
- an α-helix
Similar variants
- MLNR p.Ala164Thr Uncertain significance ★ ⚠ same type
- MLNR p.Ala198Pro Uncertain significance ★ ⚠ same type
- MLNR p.Ala229Val Uncertain significance ★ ⚠ same type
- MLNR p.Ala364Pro Uncertain significance ★ ⚠ same type
- MLNR p.Ala406Thr Uncertain significance ★ ⚠ same type
- MLNR p.Arg102Trp Uncertain significance ★ ⚠ same type
- MLNR p.Arg112Gly Uncertain significance ★ ⚠ same type
- MLNR p.Arg112His 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/mlnr-p-ser327 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown