Is ITPR2 p.Phe772= (c.2316C>T) pathogenic?

ITPR2 p.Phe772= (c.2316C>T) is classified Likely benign in ITPR2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-19). Ultra-rare (popmax 0.0217%, amr); Associated with ITPR2-related disorder.

What condition is associated with ITPR2 p.Phe772= (c.2316C>T)?

ITPR2 p.Phe772= (c.2316C>T) is associated with ITPR2-related disorder (ClinVar).

How common is ITPR2 p.Phe772= (c.2316C>T) in the general population?

ITPR2 p.Phe772= (c.2316C>T) is ultra-rare (popmax 0.0217%, amr) (gnomAD).

ITPR2 p.Phe772=

c.2316C>T · rs191593356 · VCV3046509

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0217%, amr)

Conditions

ITPR2-related disorder

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 -0.074	GERP -3.8, phastCons 0.007
Overall
CADD	6.806	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0217% Admixed American · 13/60,022 alleles

Filtering AF 0.0127% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0101%

Overall 0.00731% 118/1,614,206 alleles · ultra-rare exomes 108/1,461,890 · genomes 10/152,316 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0217%	4,617
Remaining individualsnot grpmax-eligible	0.0128%	7,813
European (non-Finnish)	0.00771%	12,967
South Asian	0.00329%	30,359
African / African-American	0.00266%	37,530
East Asian	0.00223%	44,886

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: ITPR2
Protein: p.Phe772=
Coding: c.2316C>T
MANE Select: NM_002223
dbSNP: rs191593356
Type: single nucleotide variant
Location: chr12:26656425 (GRCh38)
Gene constraint: LOEUF 0.724 · pLI <0.01 (gnomAD)

Full ITPR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ITPR2-related disorder

Similar variants

ITPR2 c.279+6G>C Benign same condition
ITPR2 c.3122+4T>C Likely benign same condition
ITPR2 c.3552+3C>T Likely benign same condition
ITPR2 c.4381-8C>T Likely benign same condition
ITPR2 p.Ala2112= Likely benign same condition
ITPR2 p.Ala898= Benign same condition
ITPR2 p.Asp2103= Likely benign same condition
ITPR2 p.Glu815= Likely benign 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/itpr2-p-phe772 (accessed [today's date]).

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