Is SLC2A10 p.Pro440= (c.1320T>C) pathogenic?

SLC2A10 p.Pro440= (c.1320T>C) is classified Likely benign in SLC2A10 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-04). Ultra-rare (popmax 0.0406%, sas); Associated with familial thoracic aortic aneurysm and aortic dissection.

What condition is associated with SLC2A10 p.Pro440= (c.1320T>C)?

SLC2A10 p.Pro440= (c.1320T>C) is associated with familial thoracic aortic aneurysm and aortic dissection (ClinVar).

How common is SLC2A10 p.Pro440= (c.1320T>C) in the general population?

SLC2A10 p.Pro440= (c.1320T>C) is ultra-rare (popmax 0.0406%, sas) (gnomAD).

SLC2A10 p.Pro440=

Q: How is Familial thoracic aortic aneurysm and aortic dissection inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

c.1320T>C · rs775312063 · VCV3228062

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0406%, sas)

Conditions

familial thoracic aortic aneurysm and aortic dissection

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 -20	GERP -3.9
Overall
CADD	0.218	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0406% South Asian · 37/91,066 alleles

Filtering AF 0.0303% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0267%

Overall 0.00253% 37/1,461,854 alleles · ultra-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.Pro440=
Coding: c.1320T>C
MANE Select: NM_030777
dbSNP: rs775312063
Type: single nucleotide variant
Location: chr20:46726895 (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

familial thoracic aortic aneurysm and aortic dissection — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Familial thoracic aortic aneurysm and aortic dissection (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood

Similar variants

SLC2A10 p.Arg105Cys Pathogenic/Likely pathogenic ★★ same condition
SLC2A10 p.Arg132Trp Pathogenic/Likely pathogenic ★★ same condition
SLC2A10 p.Arg231Trp Pathogenic/Likely pathogenic ★★ same condition
SLC2A10 p.Arg444Ter Pathogenic/Likely pathogenic ★★ same condition
SLC2A10 p.Glu437Lys Pathogenic/Likely pathogenic ★★ same condition
SLC2A10 p.Gly426Trp Pathogenic/Likely pathogenic ★★ same condition
SLC2A10 p.Met1Leu Pathogenic/Likely pathogenic ★★ same condition
SLC2A10 p.Tyr139Ter Pathogenic/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-pro440 (accessed [today's date]).

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