Is CD83 p.Gly55Asp (c.164G>A) pathogenic?

CD83 p.Gly55Asp (c.164G>A) is classified Uncertain significance in CD83 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-12). AlphaMissense: likely benign (0.063); Very rare (popmax 0.00119%, nfe).

How common is CD83 p.Gly55Asp (c.164G>A) in the general population?

CD83 p.Gly55Asp (c.164G>A) is very rare (popmax 0.00119%, nfe) (gnomAD).

What do computational predictors say about CD83 p.Gly55Asp (c.164G>A)?

AlphaMissense predicts likely benign (score 0.063) — an in-silico prediction, not a clinical call.

CD83 p.Gly55Asp

c.164G>A · VCV4650721

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.063 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00119%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.063	likely benign
REVEL	0.037	moderately benign-leaning
SaProt	LLR -10.20	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.85	GERP -5.2
Regional constraint	o/e 1.00	unconstrained · MANE · 17 kb · p 0.99 · regional, not allelic
Overall
CADD	0.188	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 0.00119% European (non-Finnish) · 14/1,178,674 alleles

Filtering AF 0.000689% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000539%

Overall 0.000959% 14/1,460,386 alleles · very rare

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.Gly55Asp
Coding: c.164G>A
MANE Select: NM_004233
Type: single nucleotide variant
Location: chr6:14131530 (GRCh38)
Gene constraint: LOEUF 1.383 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.45 · 4 PDB
Residue 55: a disulfide bond; 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-gly55asp (accessed [today's date]).

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