Is ABCE1 p.Asp3Glu (c.9C>G) pathogenic?

ABCE1 p.Asp3Glu (c.9C>G) is classified Uncertain significance in ABCE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-04). AlphaMissense: likely benign (0.1142); Very rare (popmax 8.53e-05%, nfe).

How common is ABCE1 p.Asp3Glu (c.9C>G) in the general population?

ABCE1 p.Asp3Glu (c.9C>G) is very rare (popmax 8.53e-05%, nfe) (gnomAD).

What do computational predictors say about ABCE1 p.Asp3Glu (c.9C>G)?

AlphaMissense predicts likely benign (score 0.1142) — an in-silico prediction, not a clinical call.

ABCE1 p.Asp3Glu

c.9C>G · rs1225778553 · VCV2543506

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1142 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.53e-05%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.1142	likely benign
REVEL	0.481	indeterminate
SaProt	LLR -5.36	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 2.3	GERP -1.8, phastCons 1
Regional constraint	o/e 0.46	unconstrained · MANE · 23 kb · p 3.5e-48 · regional, not allelic
Overall
CADD	17.25	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.53e-05% European (non-Finnish) · 1/1,172,314 alleles

Overall 6.92e-05% 1/1,445,130 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: ABCE1
Protein: p.Asp3Glu
Coding: c.9C>G
MANE Select: NM_002940
dbSNP: rs1225778553
Type: single nucleotide variant
Location: chr4:145104421 (GRCh38)
Gene constraint: LOEUF 0.466 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 86.76 · 3 PDB

Full ABCE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCE1 p.Asp135Asn Uncertain significance ★★ ⚠ same type
ABCE1 p.Cys475= Benign ★★ same type
ABCE1 p.Gly110= Benign ★★ same type
ABCE1 p.Arg212Ter Uncertain significance ★ same type
ABCE1 p.Asn338His Uncertain significance ★ ⚠ same type
ABCE1 p.Asp205Gly Uncertain significance ★ ⚠ same type
ABCE1 p.Asp216Glu Uncertain significance ★ ⚠ same type
ABCE1 p.Asp444Asn Uncertain significance ★ ⚠ 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/abce1-p-asp3glu (accessed [today's date]).

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