Is CD83 p.Glu22Lys (c.64G>A) pathogenic?

CD83 p.Glu22Lys (c.64G>A) is classified Uncertain significance in CD83 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-08). AlphaMissense: likely benign (0.151); Very rare (popmax 0.00935%, afr).

How common is CD83 p.Glu22Lys (c.64G>A) in the general population?

CD83 p.Glu22Lys (c.64G>A) is very rare (popmax 0.00935%, afr) (gnomAD).

What do computational predictors say about CD83 p.Glu22Lys (c.64G>A)?

AlphaMissense predicts likely benign (score 0.151) — an in-silico prediction, not a clinical call.

CD83 p.Glu22Lys

c.64G>A · rs543401049 · VCV2324455

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.151 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00935%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.151	likely benign
REVEL	0.065	moderately benign-leaning
SaProt	LLR -8.84	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 4.2	GERP 0.17, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 17 kb · p 0.99 · regional, not allelic
Overall
CADD	19.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00935% African / African-American · 7/74,904 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00309%

Overall 0.000435% 7/1,610,562 alleles · very rare exomes 1/1,458,310 · genomes 6/152,252 · joint denominator

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.Glu22Lys
Coding: c.64G>A
MANE Select: NM_004233
dbSNP: rs543401049
Type: single nucleotide variant
Location: chr6:14117976 (GRCh38)
Gene constraint: LOEUF 1.383 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.45 · 4 PDB
Residue 22: a β-strand; the ig-like v-type domain

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-glu22lys (accessed [today's date]).

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