MVD p.Lys368=
c.1104A>G · rs148833471 · VCV790328
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.861%, 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 -0.8 | GERP -2.8 |
| Overall | ||
| CADD | 0.315 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.861%
European (non-Finnish) · 10,120/1,175,866 alleles
Filtering AF
0.847%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.841%
Overall
0.717%
11,462/1,599,146 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.861% | 116 |
| Finnishnot grpmax-eligible | 0.683% | 146 |
| Remaining individualsnot grpmax-eligible | 0.54% | 185 |
| Admixed American | 0.33% | 303 |
| Ashkenazi Jewishnot grpmax-eligible | 0.324% | 308 |
| South Asian | 0.225% | 444 |
| Middle Eastern | 0.183% | 547 |
| African / African-American | 0.121% | 829 |
| East Asian | 0.0045% | 22,235 |
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
- MVD
- Protein
- p.Lys368=
- Coding
- c.1104A>G
- MANE Select
- NM_002461
- dbSNP
- rs148833471
- Type
- single nucleotide variant
- Location
- chr16:88653318 (GRCh38)
- Gene constraint
- LOEUF 1.706 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.52 · 1 PDB
- Residue 368
- a β-strand
Similar variants
- MVD p.Phe249Ser Pathogenic ★★ same type
- MVD p.Thr120Met Uncertain significance ★★ ⚠ same type
- MVD p.Arg78= Benign ★★ same type
- MVD p.Pro77= Benign ★★ same type
- MVD c.1013+1G>T Pathogenic ★ same type
- MVD c.1014-1G>T Likely pathogenic ★ same type
- MVD p.Asn292Ser Pathogenic ★ ⚠ same type
- MVD c.1013+5G>T 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/mvd-p-lys368 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown