Is CSDE1 p.Glu541= (c.1623A>G) pathogenic?

CSDE1 p.Glu541= (c.1623A>G) is classified Likely benign in CSDE1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-01). Ultra-rare (popmax 0.0165%, mid); Associated with CSDE1-related disorder.

What condition is associated with CSDE1 p.Glu541= (c.1623A>G)?

CSDE1 p.Glu541= (c.1623A>G) is associated with CSDE1-related disorder (ClinVar).

How common is CSDE1 p.Glu541= (c.1623A>G) in the general population?

CSDE1 p.Glu541= (c.1623A>G) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

CSDE1 p.Glu541=

c.1623A>G · rs749419444 · VCV3044134

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Conditions

CSDE1-related disorder

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 2.4	GERP 0.28, phastCons 1
Overall
CADD	9.115	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,064 alleles

Filtering AF 0.00818% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00635%

Overall 0.00137% 22/1,607,990 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,064
African / African-American	0.0147%	6,784
Remaining individualsnot grpmax-eligible	0.00482%	20,752
South Asian	0.00112%	89,318
European (non-Finnish)	0.000509%	196,291

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.Glu541=
Coding: c.1623A>G
MANE Select: NM_001007553
dbSNP: rs749419444
Type: single nucleotide variant
Location: chr1:114726228 (GRCh38)
Gene constraint: LOEUF 0.295 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 80.05 · 5 PDB
Residue 541: a β-strand; the csd 7 domain

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.Arg77Ter Uncertain significance same condition
CSDE1 p.Asp644Tyr Uncertain significance ⚠ same condition
CSDE1 c.2052+8C>T 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-glu541 (accessed [today's date]).

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