Is CD207 p.Asn134= (c.402C>T) pathogenic?

CD207 p.Asn134= (c.402C>T) is classified Uncertain significance in CD207 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-03-30). Ultra-rare (popmax 0.0134%, eas); Associated with Birbeck granule deficiency.

What condition is associated with CD207 p.Asn134= (c.402C>T)?

CD207 p.Asn134= (c.402C>T) is associated with Birbeck granule deficiency (ClinVar).

How common is CD207 p.Asn134= (c.402C>T) in the general population?

CD207 p.Asn134= (c.402C>T) is ultra-rare (popmax 0.0134%, eas) (gnomAD).

CD207 p.Asn134=

c.402C>T · rs782591870 · VCV625908

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, eas)

Conditions

Birbeck granule deficiency

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 -0.97	GERP -3.7
Overall
CADD	5.496	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0134% East Asian · 6/44,892 alleles

Filtering AF 0.00579% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00394%

Overall 0.000805% 13/1,613,944 alleles · ultra-rare exomes 13/1,461,674 · genomes 0/152,270 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0134%	7,482
South Asian	0.0022%	45,541
Admixed American	0.00167%	60,012
European (non-Finnish)	0.000339%	294,969

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.Asn134=
Coding: c.402C>T
MANE Select: NM_015717
dbSNP: rs782591870
Type: single nucleotide variant
Location: chr2:70833809 (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

Disease context

Birbeck granule deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CD207 p.Trp264Arg Uncertain significance ★ ⚠ same condition
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-asn134 (accessed [today's date]).

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