ERLIN2 p.Lys232=
c.696G>A · rs138164407 · VCV129022
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
rare (popmax 0.644%, nfe)
Conditions
2
Spastic paraplegia
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 1.6 | GERP 0.71, phastCons 1 |
| Overall | ||
| CADD | 7.725 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.644%
European (non-Finnish) · 7,601/1,179,796 alleles
Filtering AF
0.632%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.627%
Overall
0.517%
8,345/1,613,940 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.644% | 155 |
| Remaining individualsnot grpmax-eligible | 0.454% | 220 |
| Finnishnot grpmax-eligible | 0.23% | 436 |
| South Asian | 0.2% | 500 |
| African / African-American | 0.0879% | 1,137 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0878% | 1,139 |
| Admixed American | 0.0616% | 1,622 |
| Middle Eastern | 0.033% | 3,028 |
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
- ERLIN2
- Protein
- p.Lys232=
- Coding
- c.696G>A
- MANE Select
- NM_007175
- dbSNP
- rs138164407
- Type
- single nucleotide variant
- Location
- chr8:37751672 (GRCh38)
- Gene constraint
- LOEUF 0.703 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.35 · 5 PDB
- Residue 232
- the 'interaction with erlin1' region
Similar variants
- ERLIN2 p.Ala151Val Pathogenic/Likely pathogenic ★★ same condition
- ERLIN2 p.Gln63Lys Pathogenic/Likely pathogenic ★★ same condition
- ERLIN2 c.298+5G>A Uncertain significance ★★ same condition
- ERLIN2 c.819+3A>G Uncertain significance ★★ same condition
- ERLIN2 p.Ala290Val Uncertain significance ★★ ⚠ same condition
- ERLIN2 p.Ala99Thr Uncertain significance ★★ ⚠ same condition
- ERLIN2 p.Asn93Asp Uncertain significance ★★ ⚠ same condition
- ERLIN2 p.Gln154Pro 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/erlin2-p-lys232 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown