Is LY75-CD302 p.Ser1840Pro (c.5518T>C) pathogenic?

LY75-CD302 p.Ser1840Pro (c.5518T>C) is classified Uncertain significance in LY75-CD302 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-19). AlphaMissense: likely benign (0.0867); Absent from gnomAD v4.1.

How common is LY75-CD302 p.Ser1840Pro (c.5518T>C) in the general population?

LY75-CD302 p.Ser1840Pro (c.5518T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about LY75-CD302 p.Ser1840Pro (c.5518T>C)?

AlphaMissense predicts likely benign (score 0.0867) — an in-silico prediction, not a clinical call.

LY75-CD302 p.Ser1840Pro

c.5518T>C · VCV3292355

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0867 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0867	likely benign
REVEL	0.094	moderately benign-leaning
SaProt	LLR -12.21	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 3	GERP 1.7, phastCons 0.89
Overall
CADD	19.48	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM S199P vs ClinVar S1840P) — verify the residue.

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: LY75-CD302
Protein: p.Ser1840Pro
Coding: c.5518T>C
MANE Select: NM_014880 · reported on NM_001198759
Type: single nucleotide variant
Location: chr2:159771955 (GRCh38)

Full LY75-CD302 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/ly75-cd302-p-ser1840pro (accessed [today's date]).

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