ENPP6 p.Gly106=
c.318C>T · rs758733703 · VCV2655207
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0493%, mid)
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 -2.4 | GERP -2.9 |
| Overall | ||
| CADD | 0.604 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0493%
Middle Eastern · 3/6,084 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00715%
Overall
0.0013%
21/1,614,020 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0493% | 2,028 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
| African / African-American | 0.00267% | 37,455 |
| East Asian | 0.00223% | 44,894 |
| European (non-Finnish) | 0.0011% | 90,771 |
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
- ENPP6
- Protein
- p.Gly106=
- Coding
- c.318C>T
- MANE Select
- NM_153343
- dbSNP
- rs758733703
- Type
- single nucleotide variant
- Location
- chr4:184153657 (GRCh38)
- Gene constraint
- LOEUF 0.997 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.06
Similar variants
- ENPP6 p.Ser71= Benign ★★ same type
- ENPP6 p.Ala20Asp Uncertain significance ★ ⚠ same type
- ENPP6 p.Ala20Thr Uncertain significance ★ ⚠ same type
- ENPP6 p.Ala212Thr Uncertain significance ★ ⚠ same type
- ENPP6 p.Ala303Pro Uncertain significance ★ ⚠ same type
- ENPP6 p.Ala369Gly Uncertain significance ★ ⚠ same type
- ENPP6 p.Ala380Pro Uncertain significance ★ ⚠ same type
- ENPP6 p.Arg181Pro 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/enpp6-p-gly106 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown