Is JPH2 p.Arg498= (c.1494G>A) pathogenic?

JPH2 p.Arg498= (c.1494G>A) is classified Likely benign in JPH2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-08). No allele count reported in gnomAD v4.1 (AN 1,395,938).

How common is JPH2 p.Arg498= (c.1494G>A) in the general population?

JPH2 p.Arg498= (c.1494G>A) is no allele count reported in gnomAD v4.1 (AN 1,395,938) (gnomAD).

JPH2 p.Arg498=

c.1494G>A · VCV4684419

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,395,938)

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 -0.16	GERP -1.5, phastCons 0.31
Overall
CADD	5.411	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,395,938). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: JPH2
Protein: p.Arg498=
Coding: c.1494G>A
MANE Select: NM_020433
Type: single nucleotide variant
Location: chr20:44116181 (GRCh38)
Gene constraint: LOEUF 1.051 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.09 · 2 PDB
Residue 498: the 'disordered' region; a UniProt-annotated variant site (in cmd2e; uncertain significance)

Full JPH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

JPH2 p.Arg498Gly Uncertain significance ★ ⚠ same residue
JPH2 p.Thr161Lys Pathogenic/Likely pathogenic ★★ same type
JPH2 c.1169+5G>A Uncertain significance ★★ same type
JPH2 c.-4T>A Uncertain significance ★★ same type
JPH2 c.*15A>T Uncertain significance ★★ same type
JPH2 p.Ala181Thr Uncertain significance ★★ ⚠ same type
JPH2 p.Ala194Ser Uncertain significance ★★ ⚠ same type
JPH2 p.Ala214Glu 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/jph2-p-arg498 (accessed [today's date]).

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