LRRC7 p.Pro12=
c.36G>A · rs115352313 · VCV2638874
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.572%, eas)
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 -0.63 | GERP -3.8 |
| Overall | ||
| CADD | 6.213 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.572%
East Asian · 255/44,618 alleles
Filtering AF
0.542%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.538%
Overall
0.467%
7,480/1,603,404 alleles · rare
exomes 6,964/1,451,330 · genomes 516/152,074 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.572% | 175 |
| European (non-Finnish) | 0.554% | 181 |
| Remaining individualsnot grpmax-eligible | 0.411% | 244 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| Finnishnot grpmax-eligible | 0.216% | 463 |
| South Asian | 0.179% | 560 |
| Admixed American | 0.126% | 795 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0987% | 1,013 |
| African / African-American | 0.0789% | 1,267 |
| Middle Eastern | 0.0661% | 1,513 |
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
- LRRC7
- Protein
- p.Pro12=
- Coding
- c.36G>A
- MANE Select
- NM_001370785
- dbSNP
- rs115352313
- Type
- single nucleotide variant
- Location
- chr1:69678414 (GRCh38)
- Gene constraint
- LOEUF 0.203 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 52.05 · 2 PDB
Similar variants
- LRRC7 p.Ala1105Thr Uncertain significance ★★ same type
- LRRC7 p.Ser354Ala Uncertain significance ★★ same type
- LRRC7 p.Arg417= Likely benign ★★ same type
- LRRC7 c.787-1G>T Pathogenic ★ same type
- LRRC7 p.Gln748Ter Pathogenic ★ same type
- LRRC7 p.Gly1049Ter Pathogenic ★ same type
- LRRC7 p.Leu122Arg Likely pathogenic ★ same type
- LRRC7 c.1005-7T>A 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/lrrc7-p-pro12 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown