Is CSDE1 p.Arg792fs (c.2374del) pathogenic?

CSDE1 p.Arg792fs (c.2374del) is classified Uncertain significance in CSDE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-30). Very rare (popmax 0.00535%, afr).

How common is CSDE1 p.Arg792fs (c.2374del) in the general population?

CSDE1 p.Arg792fs (c.2374del) is very rare (popmax 0.00535%, afr) (gnomAD).

CSDE1 p.Arg792fs

c.2374del · rs1311412281 · VCV1697143

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00535%, afr)

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	escapes	premature termination codon in the last exon (20 of 20) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.8	GERP 2.6, phastCons 1
Overall
CADD	34.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00535% African / African-American · 4/74,780 alleles

Filtering AF 0.00175% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00104%

Overall 0.000248% 4/1,613,638 alleles · very rare

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: CSDE1
Protein: p.Arg792fs
Coding: c.2374del
MANE Select: NM_001007553
dbSNP: rs1311412281
Type: Deletion
Location: chr1:114718192 (GRCh38)
Gene constraint: LOEUF 0.295 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 80.05 · 5 PDB

Full CSDE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CSDE1 p.Arg792Cys Likely benign ★ ⚠ same residue
CSDE1 c.1-1710del Pathogenic ★ same type
CSDE1 p.Asn689fs Pathogenic ★ same type
CSDE1 c.403-13_403-10del Uncertain significance ★ same type
CSDE1 c.838-19del Likely benign ★ same type
CSDE1 c.310-11_310-10del Likely benign same type

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/csde1-p-arg792fs (accessed [today's date]).

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