Is CD83 p.Arg182Gln (c.545G>A) pathogenic?

CD83 p.Arg182Gln (c.545G>A) is classified Benign in CD83 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-31). AlphaMissense: likely benign (0.0736); Low-frequency (popmax 4.73%, afr).

How common is CD83 p.Arg182Gln (c.545G>A) in the general population?

CD83 p.Arg182Gln (c.545G>A) is low-frequency (popmax 4.73%, afr) (gnomAD).

What do computational predictors say about CD83 p.Arg182Gln (c.545G>A)?

AlphaMissense predicts likely benign (score 0.0736) — an in-silico prediction, not a clinical call.

CD83 p.Arg182Gln

c.545G>A · rs2230193 · VCV782470

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0736 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 4.73%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0736	likely benign
REVEL	0.036	moderately benign-leaning
SaProt	LLR -6.16	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.046	GERP -5
Regional constraint	o/e 1.00	unconstrained · MANE · 17 kb · p 0.99 · regional, not allelic
Overall
CADD	13.31	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 4.73% African / African-American · 3,551/75,010 alleles

Filtering AF 4.6% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.55%

Overall 0.249% 4,017/1,613,782 alleles · low-frequency exomes 1,961/1,461,518 · genomes 2,056/152,264 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	4.73%	21
Ashkenazi Jewishnot grpmax-eligible	0.314%	318
Remaining individualsnot grpmax-eligible	0.264%	379
Admixed American	0.23%	435
Middle Eastern	0.099%	1,010
European (non-Finnish)	0.00509%	19,662
South Asian	0.00439%	22,769

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: CD83
Protein: p.Arg182Gln
Coding: c.545G>A
MANE Select: NM_004233
dbSNP: rs2230193
Type: single nucleotide variant
Location: chr6:14135163 (GRCh38)
Gene constraint: LOEUF 1.383 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.45 · 4 PDB
Residue 182: a UniProt-annotated variant site (in)

Full CD83 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD83 p.Ala143Val Uncertain significance ★ ⚠ same type
CD83 p.Ala84Ser Uncertain significance ★ ⚠ same type
CD83 p.Ala84Thr Uncertain significance ★ ⚠ same type
CD83 p.Arg167Gln Uncertain significance ★ ⚠ same type
CD83 p.Asn191Asp Uncertain significance ★ ⚠ same type
CD83 p.Asn79His Uncertain significance ★ ⚠ same type
CD83 p.Asn79Ile Uncertain significance ★ ⚠ same type
CD83 p.Asp30Asn 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/cd83-p-arg182gln (accessed [today's date]).

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