Is CD207 p.Ala55Val (c.164C>T) pathogenic?

CD207 p.Ala55Val (c.164C>T) is classified Benign in CD207 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-18). AlphaMissense: likely benign (0.0958); Common (popmax 38.8%, amr) — too common for a highly-penetrant pathogenic allele; Associated with CD207-related disorder.

What condition is associated with CD207 p.Ala55Val (c.164C>T)?

CD207 p.Ala55Val (c.164C>T) is associated with CD207-related disorder (ClinVar).

What do computational predictors say about CD207 p.Ala55Val (c.164C>T)?

AlphaMissense predicts likely benign (score 0.0958) — an in-silico prediction, not a clinical call.

CD207 p.Ala55Val

Q: How common is CD207 p.Ala55Val (c.164C>T) in the general population?

CD207 p.Ala55Val (c.164C>T) is common (popmax 38.8%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.164C>T · rs10489990 · VCV3059383

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0958 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 38.8%, amr) — too common for a highly-penetrant pathogenic allele

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

CD207-related disorder

Computational evidence

Protein change
AlphaMissense	0.0958	likely benign
REVEL	0.037	moderately benign-leaning
SaProt	LLR -6.00	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 4.8	GERP 0.93, phastCons 0.99
Regional constraint	o/e 0.98	unconstrained · MANE · 4,723 bp · p 0.62 · regional, not allelic
Overall
CADD	16.59	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 38.8% Admixed American · 23,256/59,956 alleles

Filtering AF 38.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 38.2%

Overall 34.1% 550,116/1,612,328 alleles · common exomes 504,847/1,460,232 · genomes 45,269/152,096 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	38.8%	3
Ashkenazi Jewishnot grpmax-eligible	38%	3
Middle Eastern	35.7%	3
European (non-Finnish)	35.6%	3
Amishnot grpmax-eligible	34.9%	3
Remaining individualsnot grpmax-eligible	33.4%	3
Finnishnot grpmax-eligible	33.3%	3
East Asian	30.8%	3
South Asian	28.7%	3
African / African-American	15.5%	6

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.Ala55Val
Coding: c.164C>T
MANE Select: NM_015717
dbSNP: rs10489990
Type: single nucleotide variant
Location: chr2:70835517 (GRCh38)
Gene constraint: LOEUF 1.205 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.13 · 22 PDB
Residue 55: a UniProt-annotated variant site (in)

Full CD207 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CD207-related disorder

Similar variants

CD207 p.Ala55Thr Uncertain significance ★ ⚠ same residue
CD207 p.Ala61= Likely benign same condition
CD207 p.Gln136Glu Benign same condition
CD207 p.Glu114Val Benign same condition
CD207 p.Pro328= Benign same condition
CD207 p.Ser237= Benign same condition
CD207 p.Thr314= Benign same condition
CD207 p.Val278Ala 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-ala55val (accessed [today's date]).

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