Is CD300A p.Ser269Pro (c.805T>C) pathogenic?

CD300A p.Ser269Pro (c.805T>C) is classified Uncertain significance in CD300A (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-19). AlphaMissense: likely benign (0.2172); Absent from gnomAD v4.1.

How common is CD300A p.Ser269Pro (c.805T>C) in the general population?

CD300A p.Ser269Pro (c.805T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD300A p.Ser269Pro (c.805T>C)?

AlphaMissense predicts likely benign (score 0.2172) — an in-silico prediction, not a clinical call.

CD300A p.Ser269Pro

c.805T>C · VCV4222805

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2172 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2172	likely benign
REVEL	0.118	moderately benign-leaning
SaProt	LLR -9.65	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 0.097	GERP -3.4
Regional constraint	o/e 0.90	unconstrained · MANE · 17 kb · p 0.069 · regional, not allelic
Overall
CADD	16.84	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: CD300A
Protein: p.Ser269Pro
Coding: c.805T>C
MANE Select: NM_007261
Type: single nucleotide variant
Location: chr17:74484031 (GRCh38)
Gene constraint: LOEUF 0.932 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.59 · 1 PDB

Full CD300A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD300A p.Ser269Leu Uncertain significance ★ ⚠ same residue
CD300A p.Ala6Thr Uncertain significance ★ ⚠ same type
CD300A p.Ala98Gly Uncertain significance ★ ⚠ same type
CD300A p.Arg262Gly Uncertain significance ★ ⚠ same type
CD300A p.Arg285Pro Uncertain significance ★ ⚠ same type
CD300A p.Asn176Tyr Uncertain significance ★ ⚠ same type
CD300A p.Cys103Tyr Uncertain significance ★ ⚠ same type
CD300A p.Cys15Tyr 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/cd300a-p-ser269pro (accessed [today's date]).

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