Is CSDE1 p.Arg792Cys (c.2374C>T) pathogenic?

CSDE1 p.Arg792Cys (c.2374C>T) is classified Likely benign in CSDE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-07). AlphaMissense: likely benign (0.1862); Ultra-rare (popmax 0.0164%, mid); Associated with Inborn genetic diseases.

What condition is associated with CSDE1 p.Arg792Cys (c.2374C>T)?

CSDE1 p.Arg792Cys (c.2374C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CSDE1 p.Arg792Cys (c.2374C>T) in the general population?

CSDE1 p.Arg792Cys (c.2374C>T) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

What do computational predictors say about CSDE1 p.Arg792Cys (c.2374C>T)?

AlphaMissense predicts likely benign (score 0.1862) — an in-silico prediction, not a clinical call.

CSDE1 p.Arg792Cys

c.2374C>T · VCV4007288

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1862 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1862	likely benign
REVEL	0.498	indeterminate
SaProt	LLR -8.33	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP -0.13, phastCons 1
Regional constraint	o/e 0.62	unconstrained · MANE · 8,076 bp · p 4.1e-12 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,082 alleles

Filtering AF 0.00543% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00381%

Overall 0.00198% 32/1,613,852 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,082
Admixed American	0.0117%	8,569
East Asian	0.00668%	14,966
African / African-American	0.00534%	18,709
Remaining individualsnot grpmax-eligible	0.0048%	20,827
Finnishnot grpmax-eligible	0.00156%	63,976
European (non-Finnish)	0.0011%	90,770

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.Arg792Cys
Coding: c.2374C>T
MANE Select: NM_001007553
Type: single nucleotide variant
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

Disease context

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

Similar variants

CSDE1 p.Ala765Thr Uncertain significance ★★ ⚠ same condition
CSDE1 p.Arg132His Uncertain significance ★★ ⚠ same condition
CSDE1 p.Glu335Gly Uncertain significance ★★ same condition
CSDE1 c.2350-5C>A Benign/Likely benign ★★ same condition
CSDE1 p.Ile200Phe Likely pathogenic ★ same condition
CSDE1 c.1-1653C>G Uncertain significance ★ same condition
CSDE1 c.1-1661G>C Uncertain significance ★ same condition
CSDE1 c.1-1687A>G 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/csde1-p-arg792cys (accessed [today's date]).

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