Is ENPP3 p.Pro218Leu (c.653C>T) pathogenic?

ENPP3 p.Pro218Leu (c.653C>T) is classified Uncertain significance in ENPP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-01). AlphaMissense: ambiguous (0.4487); Ultra-rare (popmax 0.0901%, afr).

How common is ENPP3 p.Pro218Leu (c.653C>T) in the general population?

ENPP3 p.Pro218Leu (c.653C>T) is ultra-rare (popmax 0.0901%, afr) (gnomAD).

What do computational predictors say about ENPP3 p.Pro218Leu (c.653C>T)?

AlphaMissense predicts ambiguous (score 0.4487) — an in-silico prediction, not a clinical call.

ENPP3 p.Pro218Leu

c.653C>T · rs751737303 · VCV2378631

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4487 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0901%, afr)

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.4487	ambiguous
REVEL	0.799	moderately pathogenic-leaning
SaProt	LLR -11.94	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense makes no call.
Splicing
SpliceAI	Δ0.36	acceptor loss, 10 bp away · masked 0 · deltas
Pangolin	Δ0.37	loss · gain 0.00 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 4.9	GERP 1.9, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 110 kb · p 0.42 · regional, not allelic
Overall
CADD	25.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0901% African / African-American · 65/72,164 alleles

Filtering AF 0.0725% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0661%

Overall 0.0044% 68/1,545,264 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0901%	1,110
Remaining individualsnot grpmax-eligible	0.00333%	30,000
East Asian	0.00225%	44,352

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: ENPP3
Protein: p.Pro218Leu
Coding: c.653C>T
MANE Select: NM_005021
dbSNP: rs751737303
Type: single nucleotide variant
Location: chr6:131674172 (GRCh38)
Gene constraint: LOEUF 1.211 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.50 · 3 PDB
Residue 218: a disulfide bond; the 'phosphodiesterase' region; an α-helix

Full ENPP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ENPP3 c.762+4T>C Likely benign ★★ same type
CTAGE9 p.Ala668Thr Uncertain significance ★ ⚠ same type
CTAGE9 p.Asp478Tyr Uncertain significance ★ ⚠ same type
CTAGE9 p.Glu332Lys Uncertain significance ★ ⚠ same type
CTAGE9 p.Glu414Asp Uncertain significance ★ ⚠ same type
CTAGE9 p.Ile207Thr Uncertain significance ★ ⚠ same type
ENPP3 p.Ala248Asp Uncertain significance ★ ⚠ same type
ENPP3 p.Ala330Pro 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/enpp3-p-pro218leu (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown