Is CD207 p.Val119Met (c.355G>A) pathogenic?

CD207 p.Val119Met (c.355G>A) is classified Uncertain significance in CD207 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-13). AlphaMissense: likely benign (0.1044); Ultra-rare (popmax 0.0466%, amr).

How common is CD207 p.Val119Met (c.355G>A) in the general population?

CD207 p.Val119Met (c.355G>A) is ultra-rare (popmax 0.0466%, amr) (gnomAD).

What do computational predictors say about CD207 p.Val119Met (c.355G>A)?

AlphaMissense predicts likely benign (score 0.1044) — an in-silico prediction, not a clinical call.

CD207 p.Val119Met

c.355G>A · rs185940860 · VCV2595045

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1044 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0466%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1044	likely benign
REVEL	0.056	moderately benign-leaning
SaProt	LLR -6.92	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 -1.9	GERP -1.6
Regional constraint	o/e 0.98	unconstrained · MANE · 4,723 bp · p 0.62 · regional, not allelic
Overall
CADD	3.72	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 0.0466% Admixed American · 28/60,026 alleles

Filtering AF 0.0331% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0286%

Overall 0.00235% 38/1,613,956 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0466%	2,144
Remaining individualsnot grpmax-eligible	0.0128%	7,810
African / African-American	0.00133%	75,056
European (non-Finnish)	8.48e-05%	1,179,830

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.Val119Met
Coding: c.355G>A
MANE Select: NM_015717
dbSNP: rs185940860
Type: single nucleotide variant
Location: chr2:70833856 (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-val119met (accessed [today's date]).

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