Is ITPR1 p.Ser813= (c.2439G>A) pathogenic?

ITPR1 p.Ser813= (c.2439G>A) is classified Benign/Likely benign in ITPR1 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-03-01). Rare (popmax 0.894%, afr); Associated with autosomal dominant cerebellar ataxia.

What condition is associated with ITPR1 p.Ser813= (c.2439G>A)?

ITPR1 p.Ser813= (c.2439G>A) is associated with autosomal dominant cerebellar ataxia (ClinVar).

How common is ITPR1 p.Ser813= (c.2439G>A) in the general population?

ITPR1 p.Ser813= (c.2439G>A) is rare (popmax 0.894%, afr) (gnomAD).

ITPR1 p.Ser813=

c.2439G>A · rs35946460 · VCV345715

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.894%, afr)

Conditions

autosomal dominant cerebellar ataxia

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 -20	GERP -4.3
Overall
CADD	0.261	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.894% African / African-American · 670/74,910 alleles

Filtering AF 0.838% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.816%

Overall 0.0492% 792/1,608,428 alleles · rare exomes 390/1,456,242 · genomes 402/152,186 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.894%	112
Middle Eastern	0.116%	863
Remaining individualsnot grpmax-eligible	0.0771%	1,297
Admixed American	0.0484%	2,066
European (non-Finnish)	0.00306%	32,654
South Asian	0.0022%	45,392

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: ITPR1
Protein: p.Ser813=
Coding: c.2439G>A
MANE Select: NM_001378452
dbSNP: rs35946460
Type: single nucleotide variant
Location: chr3:4673370 (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

autosomal dominant cerebellar ataxia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ITPR1 p.Ser813Leu Uncertain significance ★ same residue
ITPR1 c.*1531G>A Uncertain significance ★★ same condition
ITPR1 p.Arg1761Gln Uncertain significance ★★ same condition
ITPR1 p.Arg343Lys Uncertain significance ★★ same condition
ITPR1 p.Asp1959Asn Uncertain significance ★★ same condition
ITPR1 p.Glu2128Val Uncertain significance ★★ ⚠ same condition
ITPR1 p.Gly1782Arg Uncertain significance ★★ same condition
ITPR1 p.Met2750Val Uncertain significance ★★ 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-ser813 (accessed [today's date]).

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