ENPP1 p.Phe832=
c.2496T>C · rs764192747 · VCV2171835
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0264%, sas)
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 0.39 | GERP -3, phastCons 0.038 |
| Overall | ||
| CADD | 8.085 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0264%
South Asian · 24/91,080 alleles
Filtering AF
0.0181%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0154%
Overall
0.0031%
50/1,614,036 alleles · ultra-rare
exomes 47/1,461,684 · genomes 3/152,352 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0264% | 3,795 |
| East Asian | 0.0178% | 5,607 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,945 |
| European (non-Finnish) | 0.000678% | 147,487 |
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
- ENPP1
- Protein
- p.Phe832=
- Coding
- c.2496T>C
- MANE Select
- NM_006208
- dbSNP
- rs764192747
- Type
- single nucleotide variant
- Location
- chr6:131886613 (GRCh38)
- Gene constraint
- LOEUF 0.729 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 91.35 · 7 PDB
- Residue 832
- the 'nuclease-like domain' region; a β-strand
Similar variants
- ENPP1 c.2230+1G>A Pathogenic ★★ same type
- ENPP1 c.2608-1G>A Likely pathogenic ★★ same type
- ENPP1 c.313+1G>A Pathogenic/Likely pathogenic ★★ same type
- ENPP1 c.715+1G>C Pathogenic/Likely pathogenic ★★ same type
- ENPP1 p.Arg456Ter Pathogenic/Likely pathogenic ★★ same type
- ENPP1 p.Arg476Ter Pathogenic ★★ same type
- ENPP1 p.Arg481Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- ENPP1 p.Arg782Ter Pathogenic ★★ 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/enpp1-p-phe832 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown