Is CD209 p.Gln244Arg (c.731A>G) pathogenic?

CD209 p.Gln244Arg (c.731A>G) is classified Likely benign in CD209 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-01). AlphaMissense: likely benign (0.0663); Ultra-rare (popmax 0.0415%, afr).

How common is CD209 p.Gln244Arg (c.731A>G) in the general population?

CD209 p.Gln244Arg (c.731A>G) is ultra-rare (popmax 0.0415%, afr) (gnomAD).

What do computational predictors say about CD209 p.Gln244Arg (c.731A>G)?

AlphaMissense predicts likely benign (score 0.0663) — an in-silico prediction, not a clinical call.

CD209 p.Gln244Arg

c.731A>G · rs145850292 · VCV2649173

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0663 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0415%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0663	likely benign
REVEL	0.01	strongly benign-leaning
SaProt	LLR -4.49	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 0.4	phastCons 0.001
Regional constraint	o/e 0.61	unconstrained · MANE · 437 bp · p 3.5e-06 · regional, not allelic
Overall
CADD	8.537	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 0.0415% African / African-American · 30/72,348 alleles

Filtering AF 0.0298% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0258%

Overall 0.00312% 50/1,602,798 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0415%	2,412
Remaining individualsnot grpmax-eligible	0.00483%	20,719
Finnishnot grpmax-eligible	0.00478%	20,933
East Asian	0.00225%	44,482
South Asian	0.00221%	45,286
European (non-Finnish)	0.000935%	106,919

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.Gln244Arg
Coding: c.731A>G
MANE Select: NM_021155
dbSNP: rs145850292
Type: single nucleotide variant
Location: chr19:7745535 (GRCh38)
Gene constraint: LOEUF 0.946 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.95 · 16 PDB
Residue 244: the '7 x approximate tandem repeats' region

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

Similar variants

CD209 p.Gln244Glu Uncertain significance ★ ⚠ same residue
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-gln244arg (accessed [today's date]).

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