MAF p.Ser165=
c.495C>T · VCV3384876
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000537%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 8 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 17.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000537%
European (non-Finnish) · 5/930,832 alleles
Filtering AF
0.000157%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000114%
Overall
0.000439%
5/1,139,942 alleles · very rare
exomes 3/992,262 · genomes 2/147,680 · 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
- MAF
- Protein
- p.Ser165=
- Coding
- c.495C>T
- MANE Select
- NM_005360
- Type
- single nucleotide variant
- Location
- chr16:79599408 (GRCh38)
- Gene constraint
- LOEUF 0.852 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 62.21
- Residue 165
- the 'represses are-mediated transcription' region
Similar variants
- MAF p.Ala302Val Pathogenic/Likely pathogenic ★★ same type
- MAF p.Arg299Cys Pathogenic/Likely pathogenic ★★ same type
- MAF p.Arg306Gly Pathogenic/Likely pathogenic ★★ same type
- MAF p.Cys305Phe Likely pathogenic ★★ same type
- MAF p.Pro59His Pathogenic/Likely pathogenic ★★ same type
- MAF p.Ser54Leu Pathogenic ★★ same type
- MAF p.Ser57Phe Likely pathogenic ★★ same type
- MAF p.Ser66Leu 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/maf-p-ser165 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown