Is CD209 p.Ala395= (c.1185C>T) pathogenic?

CD209 p.Ala395= (c.1185C>T) is classified Benign in CD209 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-06-21). Low-frequency (popmax 3.55%, afr).

How common is CD209 p.Ala395= (c.1185C>T) in the general population?

CD209 p.Ala395= (c.1185C>T) is low-frequency (popmax 3.55%, afr) (gnomAD).

CD209 p.Ala395=

c.1185C>T · rs11465394 · VCV780520

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 3.55%, afr)

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 -2.4	GERP -2.9
Overall
CADD	0.367	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.55% African / African-American · 2,663/75,014 alleles

Filtering AF 3.44% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.39%

Overall 0.198% 3,194/1,613,852 alleles · low-frequency exomes 1,558/1,461,618 · genomes 1,636/152,234 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	3.55%	28
Admixed American	0.407%	246
Middle Eastern	0.316%	317
Remaining individualsnot grpmax-eligible	0.286%	349
European (non-Finnish)	0.00712%	14,046
South Asian	0.00549%	18,215

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.Ala395=
Coding: c.1185C>T
MANE Select: NM_021155
dbSNP: rs11465394
Type: single nucleotide variant
Location: chr19:7743069 (GRCh38)
Gene constraint: LOEUF 0.946 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.95 · 16 PDB

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

Similar variants

CD209 p.Gln189Leu Uncertain significance ★★ ⚠ same type
CD209 p.Glu214Asp Uncertain significance ★★ ⚠ same type
CD209 p.Ala357= 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
CD209 p.Cys284Ser 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-ala395 (accessed [today's date]).

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