Is CD300LB p.Lys47Arg (c.140A>G) pathogenic?

CD300LB p.Lys47Arg (c.140A>G) is classified Uncertain significance in CD300LB (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-12). AlphaMissense: ambiguous (0.5436); Very rare (popmax 0.00133%, afr).

How common is CD300LB p.Lys47Arg (c.140A>G) in the general population?

CD300LB p.Lys47Arg (c.140A>G) is very rare (popmax 0.00133%, afr) (gnomAD).

What do computational predictors say about CD300LB p.Lys47Arg (c.140A>G)?

AlphaMissense predicts ambiguous (score 0.5436) — an in-silico prediction, not a clinical call.

CD300LB p.Lys47Arg

c.140A>G · VCV3488034

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5436 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Computational evidence

Protein change
AlphaMissense	0.5436	ambiguous
REVEL	0.441	indeterminate
SaProt	LLR -10.10	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 8,609 bp · p 0.06 · regional, not allelic
Overall
CADD	23.7	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 0.00133% African / African-American · 1/75,028 alleles

Overall 6.84e-05% 1/1,461,888 alleles · very rare

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: CD300LB
Protein: p.Lys47Arg
Coding: c.140A>G
MANE Select: NM_174892
Type: single nucleotide variant
Location: chr17:74525978 (GRCh38)
Gene constraint: LOEUF 1.189 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.23
Residue 47: the ig-like v-type domain; a disulfide bond

Full CD300LB gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD300LB c.-14G>T Uncertain significance ★ same type
CD300LB c.-42T>A Uncertain significance ★ same type
CD300LB c.-59G>T Uncertain significance ★ same type
CD300LB p.Ala26Ser Uncertain significance ★ ⚠ same type
CD300LB p.Ala26Val Uncertain significance ★ ⚠ same type
CD300LB p.Arg177Gly Uncertain significance ★ ⚠ same type
CD300LB p.Arg25Thr Uncertain significance ★ ⚠ same type
CD300LB p.Arg51Gln 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/cd300lb-p-lys47arg (accessed [today's date]).

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