Is CSDE1 p.Met1Val (c.1A>G) pathogenic?

CSDE1 p.Met1Val (c.1A>G) is classified Uncertain significance in CSDE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-14). Absent from gnomAD v4.1; Associated with CSDE1-related disorder.

What condition is associated with CSDE1 p.Met1Val (c.1A>G)?

CSDE1 p.Met1Val (c.1A>G) is associated with CSDE1-related disorder (ClinVar).

How common is CSDE1 p.Met1Val (c.1A>G) in the general population?

CSDE1 p.Met1Val (c.1A>G) is absent from gnomAD v4.1 (gnomAD).

CSDE1 p.Met1Val

c.1A>G · rs2524839828 · VCV2630866

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

start-loss

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

CSDE1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	start-loss	predicted loss-of-function in a LoF-intolerant gene
REVEL	0.396	indeterminate
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 7.9	GERP 2.9, phastCons 1
Overall
CADD	23.1	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CSDE1
Protein: p.Met1Val
Coding: c.1A>G
MANE Select: NM_001007553
dbSNP: rs2524839828
Type: single nucleotide variant
Location: chr1:114739890 (GRCh38)
Gene constraint: LOEUF 0.295 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 80.05 · 5 PDB
Residue 1: a modified residue (n-acetylmethionine)

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.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
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-met1val (accessed [today's date]).

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