GPR180 p.Pro153=
c.459A>G · rs74900909 · VCV3059123
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 9.21%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
1
GPR180-related disorder
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 -2.8 | GERP -5.4 |
| Overall | ||
| CADD | 3.691 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.21%
East Asian · 4,129/44,838 alleles
Filtering AF
8.97%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.88%
Overall
0.588%
9,495/1,613,630 alleles · common
exomes 8,394/1,461,282 · genomes 1,101/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 9.21% | 11 |
| Admixed American | 4.87% | 21 |
| Amishnot grpmax-eligible | 0.877% | 114 |
| Remaining individualsnot grpmax-eligible | 0.757% | 132 |
| South Asian | 0.437% | 229 |
| Finnishnot grpmax-eligible | 0.176% | 567 |
| European (non-Finnish) | 0.118% | 850 |
| African / African-American | 0.0813% | 1,230 |
| Middle Eastern | 0.033% | 3,030 |
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
- GPR180
- Protein
- p.Pro153=
- Coding
- c.459A>G
- MANE Select
- NM_180989
- dbSNP
- rs74900909
- Type
- single nucleotide variant
- Location
- chr13:94612344 (GRCh38)
- Gene constraint
- LOEUF 1.353 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.16
Disease context
GPR180-related disorder
Similar variants
- GPR180 c.145+9G>C Likely benign same condition
- GPR180 p.Ala155= Benign same condition
- GPR180 p.Asp309Gly Benign same condition
- GPR180 p.Gln385= Likely benign same condition
- GPR180 p.Leu192= Likely benign same condition
- GPR180 p.Met271Ile Benign same condition
- GPR180 p.Ser350Asn Benign same condition
- GPR180 p.Thr107= Likely benign 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/gpr180-p-pro153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown