Is CD207 p.Ala7= (c.21C>G) pathogenic?

CD207 p.Ala7= (c.21C>G) is classified Likely benign in CD207 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-17). Very rare (popmax 0.00127%, nfe).

How common is CD207 p.Ala7= (c.21C>G) in the general population?

CD207 p.Ala7= (c.21C>G) is very rare (popmax 0.00127%, nfe) (gnomAD).

CD207 p.Ala7=

c.21C>G · VCV4955481

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00127%, nfe)

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 0.33	GERP -1.2
Overall
CADD	5.796	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00127% European (non-Finnish) · 15/1,179,410 alleles

Filtering AF 0.000764% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000606%

Overall 0.00093% 15/1,612,598 alleles · very rare

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.Ala7=
Coding: c.21C>G
MANE Select: NM_015717
Type: single nucleotide variant
Location: chr2:70835756 (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.Ala7Ser Uncertain significance ★ ⚠ same residue
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

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-ala7 (accessed [today's date]).

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