LRPAP1 p.Ser205=
c.615C>T · rs199600966 · VCV791418
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.103%, 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 -1.3 | GERP -2.4 |
| Overall | ||
| CADD | 0.783 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.103%
European (non-Finnish) · 1,218/1,178,572 alleles
Filtering AF
0.0984%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0965%
Overall
0.0789%
1,271/1,611,400 alleles · rare
exomes 1,213/1,459,042 · genomes 58/152,358 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.103% | 968 |
| Remaining individualsnot grpmax-eligible | 0.0625% | 1,600 |
| African / African-American | 0.0107% | 9,373 |
| Admixed American | 0.00837% | 11,941 |
| Finnishnot grpmax-eligible | 0.00157% | 63,576 |
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
- LRPAP1
- Protein
- p.Ser205=
- Coding
- c.615C>T
- MANE Select
- NM_002337
- dbSNP
- rs199600966
- Type
- single nucleotide variant
- Location
- chr4:3518170 (GRCh38)
- Gene constraint
- LOEUF 1.375 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 75.80 · 10 PDB
Similar variants
- LRPAP1 p.Arg110Thr Uncertain significance ★★ ⚠ same type
- LRPAP1 p.Ala109= Benign/Likely benign ★★ same type
- LRPAP1 p.Asp211Asn Likely benign ★★ same type
- LRPAP1 p.Gly166= Benign ★★ same type
- LRPAP1 p.Gly166Ser Benign/Likely benign ★★ same type
- LRPAP1 p.Ile199Val Benign ★★ same type
- LRPAP1 c.751+1G>A Likely pathogenic ★ same type
- LRPAP1 c.593-98C>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/lrpap1-p-ser205 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown