Is CD300LD p.Val184Ile (c.550G>A) pathogenic?

CD300LD p.Val184Ile (c.550G>A) is classified Uncertain significance in CD300LD (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-01). AlphaMissense: likely benign (0.0828); Ultra-rare (popmax 0.0109%, nfe).

How common is CD300LD p.Val184Ile (c.550G>A) in the general population?

CD300LD p.Val184Ile (c.550G>A) is ultra-rare (popmax 0.0109%, nfe) (gnomAD).

What do computational predictors say about CD300LD p.Val184Ile (c.550G>A)?

AlphaMissense predicts likely benign (score 0.0828) — an in-silico prediction, not a clinical call.

CD300LD p.Val184Ile

c.550G>A · VCV4222826

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0828 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0109%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0828	likely benign
REVEL	0.008	strongly benign-leaning
SaProt	LLR -7.52	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 -3.6	GERP -3.9
Regional constraint	o/e 0.86	unconstrained · MANE · 12 kb · p 0.036 · regional, not allelic
Overall
CADD	4.021	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

Grpmax group 0.0109% European (non-Finnish) · 128/1,179,432 alleles

Filtering AF 0.00928% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00872%

Overall 0.00862% 139/1,612,984 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0109%	9,214
South Asian	0.00991%	10,088
East Asian	0.00223%	44,876
African / African-American	0.00133%	75,002

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: CD300LD
Protein: p.Val184Ile
Coding: c.550G>A
MANE Select: NM_001115152
Type: single nucleotide variant
Location: chr17:74580037 (GRCh38)
Gene constraint: LOEUF 1.278 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.81

Full CD300LD gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD300LD-AS1 n.693C>T Uncertain significance ★ same type
CD300LD p.Ala148Val Uncertain significance ★ ⚠ same type
CD300LD p.Ala18Val Uncertain significance ★ ⚠ same type
CD300LD p.Ala56Gly Uncertain significance ★ ⚠ same type
CD300LD p.Ala56Thr Uncertain significance ★ ⚠ same type
CD300LD p.Arg193Lys Uncertain significance ★ ⚠ same type
CD300LD p.Arg52Gln Uncertain significance ★ ⚠ same type
CD300LD p.Asp57Asn 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/cd300ld-p-val184ile (accessed [today's date]).

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