Is JARID2 p.Ser97Phe (c.290C>T) pathogenic?

JARID2 p.Ser97Phe (c.290C>T) is classified Uncertain significance in JARID2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-09). AlphaMissense: likely benign (0.3123); Absent from gnomAD v4.1.

How common is JARID2 p.Ser97Phe (c.290C>T) in the general population?

JARID2 p.Ser97Phe (c.290C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about JARID2 p.Ser97Phe (c.290C>T)?

AlphaMissense predicts likely benign (score 0.3123) — an in-silico prediction, not a clinical call.

JARID2 p.Ser97Phe

c.290C>T · rs2481718884 · VCV2662150

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3123 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3123	likely benign
REVEL	0.22	benign-leaning
SaProt	LLR -8.48	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.3, phastCons 1
Regional constraint	o/e 0.77	unconstrained · MANE · 164 kb · p 0.012 · regional, not allelic
Overall
CADD	27.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: JARID2
Protein: p.Ser97Phe
Coding: c.290C>T
MANE Select: NM_004973
dbSNP: rs2481718884
Type: single nucleotide variant
Location: chr6:15410332 (GRCh38)
Gene constraint: LOEUF 0.202 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 62.74 · 17 PDB
Residue 97: the 'disordered' region

Full JARID2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

JARID2 p.Ala265Pro Uncertain significance ★★ ⚠ same type
JARID2 p.Ala844Pro Uncertain significance ★★ ⚠ same type
JARID2 p.Arg311Gly Uncertain significance ★★ ⚠ same type
JARID2 p.Asn1155Tyr Uncertain significance ★★ ⚠ same type
JARID2 p.Asn171Asp Uncertain significance ★★ ⚠ same type
JARID2 p.Asn383Ser Uncertain significance ★★ ⚠ same type
JARID2 p.Glu186Gln Uncertain significance ★★ ⚠ same type
JARID2 p.His514Arg 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/jarid2-p-ser97phe (accessed [today's date]).

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