Is ITPR1 p.Val994fs (c.2979_2980insTATA) pathogenic?

ITPR1 p.Val994fs (c.29792980insTATA) is classified Pathogenic in ITPR1 (ClinVar, Single submitter, 1 submitter). Absent from gnomAD; Associated with aniridia-cerebellar ataxia-intellectual disability syndrome.

What condition is associated with ITPR1 p.Val994fs (c.2979_2980insTATA)?

ITPR1 p.Val994fs (c.2979_2980insTATA) is associated with aniridia-cerebellar ataxia-intellectual disability syndrome (ClinVar).

How common is ITPR1 p.Val994fs (c.2979_2980insTATA) in the general population?

ITPR1 p.Val994fs (c.2979_2980insTATA) is absent from gnomAD (gnomAD).

ITPR1 p.Val994fs

c.2979_2980insTATA · rs1553689752 · VCV438828

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

aniridia-cerebellar ataxia-intellectual disability syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 25 of 62
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.92	GERP 0.87, phastCons 0.008

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: ITPR1
Protein: p.Val994fs
Coding: c.2979_2980insTATA
MANE Select: NM_001378452
dbSNP: rs1553689752
Type: Insertion
Location: chr3:4680564 (GRCh38)
Gene constraint: LOEUF 0.325 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)

Full ITPR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

aniridia-cerebellar ataxia-intellectual disability syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ITPR1 p.Val994Met Uncertain significance ★★ same residue
ITPR1 p.Val994Glu Uncertain significance ★ same residue
ITPR1 p.Ala1089fs Pathogenic/Likely pathogenic ★★ same condition
ITPR1 p.Arg269Trp Pathogenic/Likely pathogenic ★★ same condition
ITPR1 p.Arg506Trp Likely pathogenic ★★ same condition
ITPR1 p.Gly2554Arg Pathogenic/Likely pathogenic ★★ same condition
ITPR1 p.Lys2611del Pathogenic ★★ same condition
ITPR1 p.Tyr567Cys Pathogenic ★★ 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/itpr1-p-val994fs (accessed [today's date]).

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