Is CD300LD p.Cys107Arg (c.319T>C) pathogenic?

CD300LD p.Cys107Arg (c.319T>C) is classified Uncertain significance in CD300LD (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-12). AlphaMissense: ambiguous (0.3447); Ultra-rare (popmax 0.0987%, afr).

How common is CD300LD p.Cys107Arg (c.319T>C) in the general population?

CD300LD p.Cys107Arg (c.319T>C) is ultra-rare (popmax 0.0987%, afr) (gnomAD).

What do computational predictors say about CD300LD p.Cys107Arg (c.319T>C)?

AlphaMissense predicts ambiguous (score 0.3447) — an in-silico prediction, not a clinical call.

CD300LD p.Cys107Arg

c.319T>C · VCV3998201

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3447 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0987%, afr)

Computational evidence

Protein change
AlphaMissense	0.3447	ambiguous · top 4% in CD300LD
REVEL	0.518	indeterminate
SaProt	LLR -12.20	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 10	GERP 2, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 12 kb · p 0.036 · regional, not allelic
Overall
CADD	24.4	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 0.0987% African / African-American · 74/75,010 alleles

Filtering AF 0.0805% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0739%

Overall 0.00508% 82/1,614,044 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0987%	1,014
Remaining individualsnot grpmax-eligible	0.0048%	20,837
Admixed American	0.00333%	30,005
European (non-Finnish)	0.000254%	393,324

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.Cys107Arg
Coding: c.319T>C
MANE Select: NM_001115152
Type: single nucleotide variant
Location: chr17:74588571 (GRCh38)
Gene constraint: LOEUF 1.278 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.81
Residue 107: the ig-like v-type domain; a disulfide bond

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-cys107arg (accessed [today's date]).

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