Is CD209 p.Arg309= (c.927A>G) pathogenic?

CD209 p.Arg309= (c.927A>G) is classified Benign in CD209 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-29). Common (popmax 11.7%, afr) — too common for a highly-penetrant pathogenic allele; Associated with CD209-related disorder.

What condition is associated with CD209 p.Arg309= (c.927A>G)?

CD209 p.Arg309= (c.927A>G) is associated with CD209-related disorder (ClinVar).

CD209 p.Arg309=

Q: How common is CD209 p.Arg309= (c.927A>G) in the general population?

CD209 p.Arg309= (c.927A>G) is common (popmax 11.7%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.927A>G · rs17159887 · VCV3039142

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 11.7%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

CD209-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5	GERP -2.8
Overall
CADD	1.221	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 11.7% African / African-American · 8,746/75,028 alleles

Filtering AF 11.5% ClinGen BA1/BS1 input FAF95, joint · FAF99 11.4%

Overall 0.956% 15,427/1,614,038 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	11.7%	9
Amishnot grpmax-eligible	5.05%	20
Admixed American	1.46%	68
Remaining individualsnot grpmax-eligible	1.37%	73
Middle Eastern	1.24%	81
European (non-Finnish)	0.388%	258
Ashkenazi Jewishnot grpmax-eligible	0.169%	592
South Asian	0.153%	655
Finnishnot grpmax-eligible	0.089%	1,123

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: CD209
Protein: p.Arg309=
Coding: c.927A>G
MANE Select: NM_021155
dbSNP: rs17159887
Type: single nucleotide variant
Location: chr19:7744193 (GRCh38)
Gene constraint: LOEUF 0.946 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.95 · 16 PDB
Residue 309: the c-type lectin domain; a disulfide bond; an α-helix

Full CD209 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CD209-related disorder

Similar variants

CD209 p.Arg221Gln Benign same condition
CD209 p.Gln189Leu Uncertain significance ★★ ⚠ same type
CD209 p.Glu214Asp Uncertain significance ★★ ⚠ same type
CD209 p.Ala357= Benign ★★ same type
CD209 p.Ala395= Benign ★★ same type
CD209 p.Asp331= Benign ★★ same type
CD209 p.Ala132Ser Uncertain significance ★ ⚠ same type
CD209 p.Ala202Val 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/cd209-p-arg309 (accessed [today's date]).

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