Is CD302 p.Leu6Arg (c.17T>G) pathogenic?

CD302 p.Leu6Arg (c.17T>G) is classified Uncertain significance in CD302 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-03). AlphaMissense: likely benign (0.1298); Absent from gnomAD v4.1.

How common is CD302 p.Leu6Arg (c.17T>G) in the general population?

CD302 p.Leu6Arg (c.17T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD302 p.Leu6Arg (c.17T>G)?

AlphaMissense predicts likely benign (score 0.1298) — an in-silico prediction, not a clinical call.

CD302 p.Leu6Arg

c.17T>G · rs1682532854 · VCV2315049

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1298 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1298	likely benign
REVEL	0.111	moderately benign-leaning
SaProt	LLR -8.45	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.22	GERP -2.6
Regional constraint	o/e 1.05	unconstrained · MANE · 26 kb · p 0.38 · regional, not allelic
Overall
CADD	15.52	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CD302
Protein: p.Leu6Arg
Coding: c.17T>G
MANE Select: NM_014880
dbSNP: rs1682532854
Type: single nucleotide variant
Location: chr2:159798182 (GRCh38)
Gene constraint: LOEUF 1.273 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.53 · 1 PDB

Full CD302 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD302 p.Ala5Thr Uncertain significance ★ ⚠ same type
CD302 p.Asp113Gly Uncertain significance ★ ⚠ same type
CD302 p.Leu9Arg Uncertain significance ★ ⚠ same type
CD302 p.Pro12Ser Uncertain significance ★ ⚠ same type
CD302 p.Pro7Arg Uncertain significance ★ ⚠ same type
LY75-CD302 p.Ser1840Pro 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/cd302-p-leu6arg (accessed [today's date]).

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