Is CD300LF p.Arg79Pro (c.236G>C) pathogenic?

CD300LF p.Arg79Pro (c.236G>C) is classified Uncertain significance in CD300LF (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-05). AlphaMissense: likely pathogenic (0.7822); Ultra-rare (popmax 0.0124%, nfe).

How common is CD300LF p.Arg79Pro (c.236G>C) in the general population?

CD300LF p.Arg79Pro (c.236G>C) is ultra-rare (popmax 0.0124%, nfe) (gnomAD).

What do computational predictors say about CD300LF p.Arg79Pro (c.236G>C)?

AlphaMissense predicts likely pathogenic (score 0.7822) — an in-silico prediction, not a clinical call.

CD300LF p.Arg79Pro

c.236G>C · rs542422427 · VCV2221572

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7822 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0124%, nfe)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.7822	likely pathogenic · top 6% in CD300LF
REVEL	0.188	benign-leaning
SaProt	LLR -16.88	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.088	GERP -3.9
Regional constraint	o/e 0.98	unconstrained · MANE · 18 kb · p 0.64 · regional, not allelic
Overall
CADD	17.88	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 0.0124% European (non-Finnish) · 146/1,180,026 alleles

Filtering AF 0.0107% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.01%

Overall 0.00954% 154/1,614,168 alleles · ultra-rare exomes 146/1,461,892 · genomes 8/152,276 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0124%	8,082
Remaining individualsnot grpmax-eligible	0.008%	12,502
African / African-American	0.00267%	37,518
Admixed American	0.00167%	60,016

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: CD300LF
Protein: p.Arg79Pro
Coding: c.236G>C
MANE Select: NM_139018
dbSNP: rs542422427
Type: single nucleotide variant
Location: chr17:74704624 (GRCh38)
Gene constraint: LOEUF 1.107 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.16 · 1 PDB
Residue 79: the ig-like v-type domain

Full CD300LF gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD300LF p.Arg79Gln Uncertain significance ★ ⚠ same residue
CD300LF p.Arg79Trp Uncertain significance ★ ⚠ same residue
CD300LF p.Ala103Val Uncertain significance ★ ⚠ same type
CD300LF p.Arg55Gln Uncertain significance ★ ⚠ same type
CD300LF p.Arg55Gly Uncertain significance ★ same type
CD300LF p.Arg89Cys Uncertain significance ★ ⚠ same type
CD300LF p.Asn88Thr Uncertain significance ★ ⚠ same type
CD300LF p.Asp102Glu 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/cd300lf-p-arg79pro (accessed [today's date]).

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