Is CSDE1 p.Arg77Ter (c.229C>T) pathogenic?

CSDE1 p.Arg77Ter (c.229C>T) is classified Uncertain significance in CSDE1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-12-12). Very rare (popmax 0.00133%, afr); Associated with CSDE1-related disorder.

What condition is associated with CSDE1 p.Arg77Ter (c.229C>T)?

CSDE1 p.Arg77Ter (c.229C>T) is associated with CSDE1-related disorder (ClinVar).

How common is CSDE1 p.Arg77Ter (c.229C>T) in the general population?

CSDE1 p.Arg77Ter (c.229C>T) is very rare (popmax 0.00133%, afr) (gnomAD).

CSDE1 p.Arg77Ter

c.229C>T · rs1660502311 · VCV3030528

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Conditions

CSDE1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 4 of 20
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.9, phastCons 1
Overall
CADD	40.0	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 0.00133% African / African-American · 1/74,960 alleles

Overall 6.84e-05% 1/1,461,408 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.Arg77Ter
Coding: c.229C>T
MANE Select: NM_001007553
dbSNP: rs1660502311
Type: single nucleotide variant
Location: chr1:114738043 (GRCh38)
Gene constraint: LOEUF 0.295 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 80.05 · 5 PDB
Residue 77: the csd 1 domain; a β-strand

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

Disease context

CSDE1-related disorder

Similar variants

CSDE1 p.Gln712Ter Likely pathogenic ★ same condition
CSDE1 p.Arg324Ter Uncertain significance ★ same condition
CSDE1 p.Arg774His Uncertain significance ★ ⚠ same condition
CSDE1 p.Met1Val Uncertain significance ★ same condition
CSDE1 p.Pro779Arg Uncertain significance ★ ⚠ same condition
CSDE1 p.Asp644Tyr Uncertain significance ⚠ same condition
CSDE1 c.2052+8C>T Likely benign same condition
CSDE1 c.*10C>G Likely benign 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-arg77ter (accessed [today's date]).

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