Is CD207 p.Arg187Gln (c.560G>A) pathogenic?

CD207 p.Arg187Gln (c.560G>A) is classified Likely benign in CD207 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-02). AlphaMissense: likely benign (0.0579); Very rare (popmax 0.00674%, amr).

How common is CD207 p.Arg187Gln (c.560G>A) in the general population?

CD207 p.Arg187Gln (c.560G>A) is very rare (popmax 0.00674%, amr) (gnomAD).

What do computational predictors say about CD207 p.Arg187Gln (c.560G>A)?

AlphaMissense predicts likely benign (score 0.0579) — an in-silico prediction, not a clinical call.

CD207 p.Arg187Gln

c.560G>A · rs551434216 · VCV2568886

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0579 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00674%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0579	likely benign
REVEL	0.014	strongly benign-leaning
SaProt	LLR -4.48	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 -3.4	GERP -3.6
Regional constraint	o/e 0.98	unconstrained · MANE · 4,723 bp · p 0.62 · regional, not allelic
Overall
CADD	5.41	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 0.00674% Admixed American · 4/59,322 alleles

Filtering AF 0.00488% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00448%

Overall 0.0051% 82/1,608,276 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00674%	14,831
European (non-Finnish)	0.00603%	16,573
South Asian	0.00332%	30,101
Remaining individualsnot grpmax-eligible	0.00321%	31,109
East Asian	0.00223%	44,796
African / African-American	0.00134%	74,838

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: CD207
Protein: p.Arg187Gln
Coding: c.560G>A
MANE Select: NM_015717
dbSNP: rs551434216
Type: single nucleotide variant
Location: chr2:70833651 (GRCh38)
Gene constraint: LOEUF 1.205 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.13 · 22 PDB

Full CD207 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD207 p.Arg66Gln Benign ★★ same type
CD207 p.Ala10Val Uncertain significance ★ ⚠ same type
CD207 p.Ala135Thr Uncertain significance ★ ⚠ same type
CD207 p.Ala152Val Uncertain significance ★ ⚠ same type
CD207 p.Ala246Glu Uncertain significance ★ ⚠ same type
CD207 p.Ala246Val Uncertain significance ★ ⚠ same type
CD207 p.Ala55Thr Uncertain significance ★ ⚠ same type
CD207 p.Ala7Ser 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/cd207-p-arg187gln (accessed [today's date]).

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