Is CD207 p.Val107Ile (c.319G>A) pathogenic?

CD207 p.Val107Ile (c.319G>A) is classified Uncertain significance in CD207 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-26). AlphaMissense: likely benign (0.0682); Ultra-rare (popmax 0.0179%, eas).

How common is CD207 p.Val107Ile (c.319G>A) in the general population?

CD207 p.Val107Ile (c.319G>A) is ultra-rare (popmax 0.0179%, eas) (gnomAD).

What do computational predictors say about CD207 p.Val107Ile (c.319G>A)?

AlphaMissense predicts likely benign (score 0.0682) — an in-silico prediction, not a clinical call.

CD207 p.Val107Ile

c.319G>A · rs782392811 · VCV2464394

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0682 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0179%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0682	likely benign
REVEL	0.003	strongly benign-leaning
SaProt	LLR -6.76	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 -11	GERP -3.7
Regional constraint	o/e 0.98	unconstrained · MANE · 4,723 bp · p 0.62 · regional, not allelic
Overall
CADD	0.002	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0179% East Asian · 8/44,720 alleles

Filtering AF 0.00886% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00643%

Overall 0.0074% 119/1,607,188 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0179%	5,590
Middle Eastern	0.0166%	6,042
African / African-American	0.00938%	10,665
Admixed American	0.0084%	11,900
European (non-Finnish)	0.00791%	12,640
Remaining individualsnot grpmax-eligible	0.00643%	15,543
Finnishnot grpmax-eligible	0.00156%	63,950

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.Val107Ile
Coding: c.319G>A
MANE Select: NM_015717
dbSNP: rs782392811
Type: single nucleotide variant
Location: chr2:70833892 (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-val107ile (accessed [today's date]).

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