GAN p.Pro315=
c.945G>A · rs139230642 · VCV533938
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0493%, mid)
Conditions
2
Inborn genetic diseases
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 -3.3 | GERP -4.8 |
| Overall | ||
| CADD | 2.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0493%
Middle Eastern · 3/6,084 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0106%
Overall
0.0108%
175/1,613,730 alleles · ultra-rare
exomes 162/1,461,586 · genomes 13/152,144 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0493% | 2,028 |
| European (non-Finnish) | 0.0129% | 7,762 |
| Admixed American | 0.0117% | 8,570 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,411 |
| African / African-American | 0.00534% | 18,724 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,604 |
| East Asian | 0.00223% | 44,898 |
| South Asian | 0.0011% | 91,076 |
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
- GAN
- Protein
- p.Pro315=
- Coding
- c.945G>A
- MANE Select
- NM_022041
- dbSNP
- rs139230642
- Type
- single nucleotide variant
- Location
- chr16:81357903 (GRCh38)
- Gene constraint
- LOEUF 0.842 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.93 · 2 PDB
- Residue 315
- a UniProt-annotated variant site (in gan1)
Similar variants
- GAN p.Pro315Arg Uncertain significance ★ ⚠ same residue
- GAN p.Pro315Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- GAN c.1502+1G>T Pathogenic/Likely pathogenic ★★ same condition
- GAN c.851+1G>A Pathogenic/Likely pathogenic ★★ same condition
- GAN p.Arg545His Pathogenic/Likely pathogenic ★★ same condition
- GAN p.Gln103Ter Pathogenic ★★ same condition
- GAN p.Glu486Lys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- GAN c.1373+4C>T Uncertain significance ★★ same condition
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/gan-p-pro315 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown