Is SLC2A10 p.Phe110= (c.330C>T) pathogenic?

SLC2A10 p.Phe110= (c.330C>T) is classified Conflicting classifications of pathogenicity in SLC2A10 (ClinVar, Conflicting submitters, 10 submitters; last evaluated 2026-02-04). Ultra-rare (popmax 0.0277%, nfe); Associated with arterial tortuosity syndrome.

What condition is associated with SLC2A10 p.Phe110= (c.330C>T)?

SLC2A10 p.Phe110= (c.330C>T) is associated with arterial tortuosity syndrome, familial thoracic aortic aneurysm and aortic dissection (ClinVar).

How common is SLC2A10 p.Phe110= (c.330C>T) in the general population?

SLC2A10 p.Phe110= (c.330C>T) is ultra-rare (popmax 0.0277%, nfe) (gnomAD).

SLC2A10 p.Phe110=

c.330C>T · rs199848479 · VCV338591

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 10 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0277%, nfe)

Conditions

arterial tortuosity syndrome

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 -9.2	GERP -3.9
Overall
CADD	1.256	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0277% European (non-Finnish) · 327/1,180,034 alleles

Filtering AF 0.0252% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0242%

Overall 0.0216% 349/1,614,116 alleles · ultra-rare exomes 332/1,461,782 · genomes 17/152,334 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0277%	3,609
East Asian	0.0156%	6,409
Remaining individualsnot grpmax-eligible	0.0144%	6,945
South Asian	0.00549%	18,217
Finnishnot grpmax-eligible	0.00156%	63,946

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: SLC2A10
Protein: p.Phe110=
Coding: c.330C>T
MANE Select: NM_030777
dbSNP: rs199848479
Type: single nucleotide variant
Location: chr20:46725366 (GRCh38)
Gene constraint: LOEUF 1.087 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 74.78

Full SLC2A10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

arterial tortuosity syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: familial thoracic aortic aneurysm and aortic dissection

Similar variants

SLC2A10 c.1411+2T>A Pathogenic/Likely pathogenic ★★ same condition
SLC2A10 p.Arg105Cys Pathogenic/Likely pathogenic ★★ same condition
SLC2A10 p.Arg132Trp Pathogenic/Likely pathogenic ★★ same condition
SLC2A10 p.Arg229Ter Pathogenic ★★ same condition
SLC2A10 p.Arg231Gln Pathogenic ★★ same condition
SLC2A10 p.Arg231Trp Pathogenic/Likely pathogenic ★★ same condition
SLC2A10 p.Arg444Ter Pathogenic/Likely pathogenic ★★ same condition
SLC2A10 p.Gln243Lys Likely pathogenic ★★ 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/slc2a10-p-phe110 (accessed [today's date]).

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