Is JADE2 p.Ser803= (c.2409C>T) pathogenic?

JADE2 p.Ser803= (c.2409C>T) is classified Likely benign in JADE2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-26). Very rare (popmax 0.00549%, sas).

How common is JADE2 p.Ser803= (c.2409C>T) in the general population?

JADE2 p.Ser803= (c.2409C>T) is very rare (popmax 0.00549%, sas) (gnomAD).

JADE2 p.Ser803=

c.2409C>T · VCV4040663

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00549%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.12	GERP -0.97, phastCons 0.93
Overall
CADD	11.24	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00549% South Asian · 5/91,092 alleles

Filtering AF 0.0021% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00136%

Overall 0.00112% 18/1,613,998 alleles · very rare exomes 16/1,461,794 · genomes 2/152,204 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00549%	18,218
Remaining individualsnot grpmax-eligible	0.0016%	62,486
European (non-Finnish)	0.00102%	98,337

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: JADE2
Protein: p.Ser803=
Coding: c.2409C>T
MANE Select: NM_001388185
Type: single nucleotide variant
Location: chr5:134579221 (GRCh38)
Gene constraint: LOEUF 0.25 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 62.79

Full JADE2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

JADE2 p.Ala439Asp Uncertain significance ★ ⚠ same type
JADE2 p.Ala439Thr Uncertain significance ★ ⚠ same type
JADE2 p.Ala668Val Uncertain significance ★ ⚠ same type
JADE2 p.Ala677Thr Uncertain significance ★ ⚠ same type
JADE2 p.Ala721Thr Uncertain significance ★ ⚠ same type
JADE2 p.Ala733Thr Uncertain significance ★ ⚠ same type
JADE2 p.Ala744Thr Uncertain significance ★ ⚠ same type
JADE2 p.Arg136His Uncertain significance ★ ⚠ same type

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/jade2-p-ser803 (accessed [today's date]).

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