Is JUP p.Ala110= (c.330C>T) pathogenic?

JUP p.Ala110= (c.330C>T) is classified Likely benign in JUP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-11). Very rare (popmax 0.00111%, sas); Associated with Cardiovascular phenotype.

What condition is associated with JUP p.Ala110= (c.330C>T)?

JUP p.Ala110= (c.330C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is JUP p.Ala110= (c.330C>T) in the general population?

JUP p.Ala110= (c.330C>T) is very rare (popmax 0.00111%, sas) (gnomAD).

JUP p.Ala110=

c.330C>T · rs2544192771 · VCV2625422

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00111%, sas)

Conditions

Cardiovascular phenotype

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 2.5	GERP 0.24, phastCons 1
Overall
CADD	10.22	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00111% South Asian · 1/90,032 alleles

Overall 6.87e-05% 1/1,456,130 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: JUP
Protein: p.Ala110=
Coding: c.330C>T
MANE Select: NM_002230
dbSNP: rs2544192771
Type: single nucleotide variant
Location: chr17:41769556 (GRCh38)
Gene constraint: LOEUF 0.533 · pLI 0.74 (gnomAD)
Structure: AlphaFold pLDDT 80.88 · 1 PDB

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

JUP p.Ala110Ser Uncertain significance ★ ⚠ same residue
JUP p.Ala110Val Uncertain significance ★★ ⚠ same residue
JUP p.Ala110Thr Uncertain significance ★ ⚠ same residue
JUP c.468+4T>C Uncertain significance ★★ same condition
JUP c.707+5C>A Uncertain significance ★★ same condition
JUP c.-1G>A Uncertain significance ★★ same condition
JUP p.Ala178Val Uncertain significance ★★ ⚠ same condition
JUP p.Ala263Val Uncertain significance ★★ ⚠ 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/jup-p-ala110 (accessed [today's date]).

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