Is JPH2 p.Ile545= (c.1635C>T) pathogenic?

JPH2 p.Ile545= (c.1635C>T) is classified Likely benign in JPH2 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-11-04). No allele count reported in gnomAD v4.1 (AN 1,573,302).

How common is JPH2 p.Ile545= (c.1635C>T) in the general population?

JPH2 p.Ile545= (c.1635C>T) is no allele count reported in gnomAD v4.1 (AN 1,573,302) (gnomAD).

JPH2 p.Ile545=

c.1635C>T · rs964166503 · VCV390507

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 1,573,302)

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 2.7	GERP 0.79, phastCons 1
Overall
CADD	10.73	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,573,302). 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.Ile545=
Coding: c.1635C>T
MANE Select: NM_020433
dbSNP: rs964166503
Type: single nucleotide variant
Location: chr20:44116040 (GRCh38)
Gene constraint: LOEUF 1.051 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.09 · 2 PDB
Residue 545: 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.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
JPH2 p.Ala23Thr 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-ile545 (accessed [today's date]).

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