Is CD209 p.Glu214Asp (c.642G>C) pathogenic?

CD209 p.Glu214Asp (c.642G>C) is classified Uncertain significance in CD209 (ClinVar, Multiple submitters, 3 submitters). AlphaMissense: likely benign (0.2826); Low-frequency (popmax 2.99%, afr); Associated with Mycobacterium tuberculosis, susceptibility to.

What condition is associated with CD209 p.Glu214Asp (c.642G>C)?

CD209 p.Glu214Asp (c.642G>C) is associated with Mycobacterium tuberculosis, susceptibility to, susceptibility to HIV infection, dengue virus, susceptibility to (ClinVar).

How common is CD209 p.Glu214Asp (c.642G>C) in the general population?

CD209 p.Glu214Asp (c.642G>C) is low-frequency (popmax 2.99%, afr) (gnomAD).

What do computational predictors say about CD209 p.Glu214Asp (c.642G>C)?

AlphaMissense predicts likely benign (score 0.2826) — an in-silico prediction, not a clinical call.

CD209 p.Glu214Asp

c.642G>C · rs11465377 · VCV625909

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.2826 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.99%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Mycobacterium tuberculosis, susceptibility to

Computational evidence

Protein change
AlphaMissense	0.2826	likely benign
REVEL	0.095	moderately benign-leaning
SaProt	LLR -8.39	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 -1.4
Regional constraint	o/e 0.61	unconstrained · MANE · 437 bp · p 3.5e-06 · regional, not allelic
Overall
CADD	7.289	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 2.99% African / African-American · 1,339/44,734 alleles

Filtering AF 2.86% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.81%

Overall 0.238% 1,467/617,376 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.99%	33
Admixed American	0.198%	505
Remaining individualsnot grpmax-eligible	0.156%	641
Middle Eastern	0.0433%	2,310
European (non-Finnish)	0.00392%	25,499
South Asian	0.00194%	51,612

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.Glu214Asp
Coding: c.642G>C
MANE Select: NM_021155
dbSNP: rs11465377
Type: single nucleotide variant
Location: chr19:7745624 (GRCh38)
Gene constraint: LOEUF 0.946 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.95 · 16 PDB
Residue 214: the '7 x approximate tandem repeats' region; a UniProt-annotated variant site (in)

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

Disease context

Mycobacterium tuberculosis, susceptibility to — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: susceptibility to HIV infection dengue virus, susceptibility to

Similar variants

CD209 p.Glu214Gly Uncertain significance ★ ⚠ same residue
CD209 p.Gln189Leu Uncertain significance ★★ ⚠ same condition
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
CD209 p.Asp75Gly 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-glu214asp (accessed [today's date]).

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