Is CASQ1 p.Asp244= (c.732C>T) pathogenic?

CASQ1 p.Asp244= (c.732C>T) is classified Likely benign in CASQ1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-04). Very rare (popmax 0.00347%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CASQ1 p.Asp244= (c.732C>T)?

CASQ1 p.Asp244= (c.732C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CASQ1 p.Asp244= (c.732C>T) in the general population?

CASQ1 p.Asp244= (c.732C>T) is very rare (popmax 0.00347%, nfe) (gnomAD).

CASQ1 p.Asp244=

c.732C>T · rs751402289 · VCV2461511

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00347%, nfe)

Conditions

Inborn genetic diseases

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 1.8	GERP 1.5, phastCons 1
Overall
CADD	9.578	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00347% European (non-Finnish) · 41/1,180,016 alleles

Filtering AF 0.00259% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00233%

Overall 0.00291% 47/1,614,034 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0064%	15,623
European (non-Finnish)grpmax	0.00347%	28,781
African / African-American	0.00267%	37,456

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CASQ1
Protein: p.Asp244=
Coding: c.732C>T
MANE Select: NM_001231
dbSNP: rs751402289
Type: single nucleotide variant
Location: chr1:160195977 (GRCh38)
Gene constraint: LOEUF 0.965 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.51 · 6 PDB
Residue 244: a UniProt-annotated variant site (in vmcqa; no effect on calcium-dependent susceptibility to proteolytic degradation; increased calcium-dependent aggregation; causes impaired polymerization of the protein; no effect on subcellular localization; decreased calcium content of sarcoplasmic reticulum stores; reduced sarcoplasmic reticulum calcium release during excitation-contraction coupling); a β-strand

Full CASQ1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CASQ1 p.Asp244Glu Uncertain significance ★ ⚠ same residue
CASQ1 p.Asp244Gly Pathogenic ★★ ⚠ same residue
CASQ1 p.Ala115Val Uncertain significance ★★ ⚠ same condition
CASQ1 p.Ala289Val Uncertain significance ★★ ⚠ same condition
CASQ1 p.Arg16Gln Uncertain significance ★★ ⚠ same condition
CASQ1 p.Arg16Trp Uncertain significance ★★ ⚠ same condition
CASQ1 p.Asp159Gly Uncertain significance ★★ ⚠ same condition
CASQ1 p.Asp309Asn 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/casq1-p-asp244 (accessed [today's date]).

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