BTNL2 p.Ser158=
c.474T>C · rs143181335 · VCV3336814
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.437%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>C here scores Δ0.28 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.3 | GERP -2.4 |
| Overall | ||
| CADD | 0.592 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.437%
South Asian · 397/90,822 alleles
Filtering AF
0.402%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.388%
Overall
0.0715%
1,151/1,610,878 alleles · rare
exomes 1,074/1,459,924 · genomes 77/150,954 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.437% | 229 |
| Middle Eastern | 0.314% | 319 |
| Remaining individualsnot grpmax-eligible | 0.0961% | 1,041 |
| European (non-Finnish) | 0.0549% | 1,820 |
| Admixed American | 0.0201% | 4,977 |
| Finnishnot grpmax-eligible | 0.0112% | 8,955 |
| African / African-American | 0.00671% | 14,902 |
| East Asian | 0.00447% | 22,367 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,584 |
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
- BTNL2
- Protein
- p.Ser158=
- Coding
- c.474T>C
- MANE Select
- NM_001304561
- dbSNP
- rs143181335
- Type
- single nucleotide variant
- Location
- chr6:32403170 (GRCh38)
- Gene constraint
- LOEUF 1.26 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.97
- Residue 158
- the ig-like v-type 2 domain
Similar variants
- BTNL2 p.Gly337Arg Uncertain significance ★★ same type
- BTNL2 p.Ala12= Benign ★★ same type
- BTNL2 c.709+6T>C Uncertain significance ★ same type
- BTNL2 c.80-284C>G Uncertain significance ★ same type
- BTNL2 p.Ala14Asp Uncertain significance ★ ⚠ same type
- BTNL2 p.Ala14Ser Uncertain significance ★ ⚠ same type
- BTNL2 p.Ala306Thr Uncertain significance ★ ⚠ same type
- BTNL2 p.Ala430Thr 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/btnl2-p-ser158 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown