Is CD207 p.Pro328= (c.984G>A) pathogenic?

CD207 p.Pro328= (c.984G>A) is classified Benign in CD207 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-21). Common (popmax 28.2%, nfe) — too common for a highly-penetrant pathogenic allele; Associated with CD207-related disorder.

What condition is associated with CD207 p.Pro328= (c.984G>A)?

CD207 p.Pro328= (c.984G>A) is associated with CD207-related disorder (ClinVar).

CD207 p.Pro328=

Q: How common is CD207 p.Pro328= (c.984G>A) in the general population?

CD207 p.Pro328= (c.984G>A) is common (popmax 28.2%, nfe) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.984G>A · rs13421115 · VCV3060971

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 28.2%, nfe) — too common for a highly-penetrant pathogenic allele

Conditions

CD207-related disorder

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 -7
Overall
CADD	0.244	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 28.2% European (non-Finnish) · 332,855/1,178,656 alleles

Filtering AF 28.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 28.1%

Overall 25.5% 411,584/1,611,962 alleles · common

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	35.2%	3
European (non-Finnish)grpmax	28.2%	4
Ashkenazi Jewishnot grpmax-eligible	27.1%	4
Middle Eastern	26.7%	4
Remaining individualsnot grpmax-eligible	24.1%	4
African / African-American	21.7%	5
Finnishnot grpmax-eligible	21.7%	5
South Asian	16.2%	6
Admixed American	14.7%	7
East Asian	0.0981%	1,020

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Pro328=
Coding: c.984G>A
MANE Select: NM_015717
dbSNP: rs13421115
Type: single nucleotide variant
Location: chr2:70831053 (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

CD207-related disorder

Similar variants

CD207 p.Ala55Val Benign same condition
CD207 p.Ala61= Likely benign same condition
CD207 p.Gln136Glu Benign same condition
CD207 p.Glu114Val Benign same condition
CD207 p.Ser237= Benign same condition
CD207 p.Thr314= Benign same condition
CD207 p.Val278Ala Benign same condition
CD207 p.Val78= Benign same condition

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-pro328 (accessed [today's date]).

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