Is CD300LB p.Val53Ala (c.158T>C) pathogenic?

CD300LB p.Val53Ala (c.158T>C) is classified Likely benign in CD300LB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-06). AlphaMissense: likely benign (0.0708); Very rare (popmax 0.00667%, amr).

How common is CD300LB p.Val53Ala (c.158T>C) in the general population?

CD300LB p.Val53Ala (c.158T>C) is very rare (popmax 0.00667%, amr) (gnomAD).

What do computational predictors say about CD300LB p.Val53Ala (c.158T>C)?

AlphaMissense predicts likely benign (score 0.0708) — an in-silico prediction, not a clinical call.

CD300LB p.Val53Ala

c.158T>C · VCV3998198

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0708 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00667%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0708	likely benign
REVEL	0.063	moderately benign-leaning
SaProt	LLR 0.19	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 -2.2	GERP -3.9
Regional constraint	o/e 0.88	unconstrained · MANE · 8,609 bp · p 0.06 · regional, not allelic
Overall
CADD	0.007	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 0.00667% Admixed American · 4/59,934 alleles

Filtering AF 0.00226% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00135%

Overall 0.00112% 18/1,613,502 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00667%	14,983
African / African-American	0.00134%	74,680
European (non-Finnish)	0.0011%	90,764

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.Val53Ala
Coding: c.158T>C
MANE Select: NM_174892
Type: single nucleotide variant
Location: chr17:74525960 (GRCh38)
Gene constraint: LOEUF 1.189 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.23
Residue 53: 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-val53ala (accessed [today's date]).

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