BLTP1 p.Arg638=
c.1914C>T · VCV4968422
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.31 | donor loss · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.47 | GERP 0.92, phastCons 1 |
| Overall | ||
| CADD | 9.936 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,726 alleles
Overall
0.000186%
3/1,611,650 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,726 |
| African / African-American | 0.00134% | 74,694 |
| European (non-Finnish) | 8.48e-05% | 1,178,916 |
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
- BLTP1
- Protein
- p.Arg638=
- Coding
- c.1914C>T
- MANE Select
- NM_001384125
- Type
- single nucleotide variant
- Location
- chr4:122209320 (GRCh38)
- Residue 638
- a UniProt-annotated variant site (in alkkucs)
Similar variants
- BLTP1 p.Arg638His Uncertain significance ★★ same residue
- BLTP1 p.Arg638Cys Uncertain significance ★ same residue
- BLTP1 p.Arg968Cys Likely pathogenic ★★ ⚠ same type
- BLTP1 c.1498+4A>G Uncertain significance ★★ same type
- BLTP1 p.Ala2332Thr Uncertain significance ★★ ⚠ same type
- BLTP1 p.Arg1317His Uncertain significance ★★ same type
- BLTP1 p.Arg1791Lys Uncertain significance ★★ ⚠ same type
- BLTP1 p.Arg2095His 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/bltp1-p-arg638 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown