Is SLC2A10 p.Ser115= (c.345C>T) pathogenic?

SLC2A10 p.Ser115= (c.345C>T) is classified Likely benign in SLC2A10 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-14). Very rare (popmax 0.00223%, eas); Associated with arterial tortuosity syndrome.

What condition is associated with SLC2A10 p.Ser115= (c.345C>T)?

SLC2A10 p.Ser115= (c.345C>T) is associated with arterial tortuosity syndrome (ClinVar).

How common is SLC2A10 p.Ser115= (c.345C>T) in the general population?

SLC2A10 p.Ser115= (c.345C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

SLC2A10 p.Ser115=

c.345C>T · VCV3624739

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

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 -1	GERP -1.3, phastCons 0.001
Overall
CADD	7.127	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,872 alleles

Overall 6.84e-05% 1/1,461,846 alleles · very rare

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.Ser115=
Coding: c.345C>T
MANE Select: NM_030777
Type: single nucleotide variant
Location: chr20:46725381 (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

Similar variants

SLC2A10 p.Ser115_Ala278delinsPro Pathogenic ★ same residue
SLC2A10 p.Ser115Phe Uncertain significance ★ ⚠ same residue
SLC2A10 p.Ser115Tyr Uncertain significance ★ ⚠ same residue
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

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-ser115 (accessed [today's date]).

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