Is STIM1 p.Phe710= (c.2130T>C) pathogenic?

STIM1 p.Phe710= (c.2130T>C) is classified Likely benign in STIM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-14). Absent from gnomAD v4.1; Associated with combined immunodeficiency due to STIM1 deficiency.

What condition is associated with STIM1 p.Phe710= (c.2130T>C)?

STIM1 p.Phe710= (c.2130T>C) is associated with combined immunodeficiency due to STIM1 deficiency, tubular aggregate myopathy, Stormorken syndrome (ClinVar).

How common is STIM1 p.Phe710= (c.2130T>C) in the general population?

STIM1 p.Phe710= (c.2130T>C) is absent from gnomAD v4.1 (gnomAD).

STIM1 p.Phe710=

Q: How is Combined immunodeficiency due to CRAC channel dysfunction inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.2130T>C · rs1554972256 · VCV461729

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

combined immunodeficiency due to STIM1 deficiency

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 5	GERP 2.6, phastCons 1
Overall
CADD	9.823	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: STIM1
Protein: p.Phe710=
Coding: c.2130T>C
MANE Select: NM_001382567
dbSNP: rs1554972256
Type: single nucleotide variant
Location: chr11:4091777 (GRCh38)
Gene constraint: LOEUF 0.475 · pLI 0.99 (gnomAD)
Structure: AlphaFold pLDDT 68.81 · 6 PDB

Full STIM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

combined immunodeficiency due to STIM1 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: tubular aggregate myopathy Stormorken syndrome

For Combined immunodeficiency due to CRAC channel dysfunction (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

STIM1 p.Arg304Trp Pathogenic ★★ ⚠ same condition
STIM1 p.Arg50Ter Pathogenic/Likely pathogenic ★★ same condition
STIM1 p.His109Arg Pathogenic/Likely pathogenic ★★ same condition
STIM1 p.Ser88Gly Pathogenic/Likely pathogenic ★★ same condition
STIM1 c.792-3C>A Uncertain significance ★★ same condition
STIM1 c.792-3C>G Uncertain significance ★★ same condition
STIM1 p.Ala163Asp Uncertain significance ★★ ⚠ same condition
STIM1 p.Ala31Pro 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/stim1-p-phe710 (accessed [today's date]).

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