Is CD300LB p.Ser192= (c.576C>T) pathogenic?

CD300LB p.Ser192= (c.576C>T) is classified Likely benign in CD300LB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-11). Ultra-rare (popmax 0.0178%, eas).

How common is CD300LB p.Ser192= (c.576C>T) in the general population?

CD300LB p.Ser192= (c.576C>T) is ultra-rare (popmax 0.0178%, eas) (gnomAD).

CD300LB p.Ser192=

c.576C>T · VCV4650574

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0178%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2	GERP -2.8
Overall
CADD	1.482	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0178% East Asian · 8/44,882 alleles

Filtering AF 0.011% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00888%

Overall 0.00242% 39/1,614,152 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0178%	5,610
South Asian	0.0176%	5,693
African / African-American	0.00666%	15,006
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,604
Remaining individualsnot grpmax-eligible	0.0016%	62,508
European (non-Finnish)	0.000678%	147,501

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.Ser192=
Coding: c.576C>T
MANE Select: NM_174892
Type: single nucleotide variant
Location: chr17:74522768 (GRCh38)
Gene constraint: LOEUF 1.189 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.23

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-ser192 (accessed [today's date]).

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