Is ABCE1 p.Ser51Phe (c.152C>T) pathogenic?

ABCE1 p.Ser51Phe (c.152C>T) is classified Uncertain significance in ABCE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-10). AlphaMissense: likely pathogenic (0.9663); Absent from gnomAD v4.1.

How common is ABCE1 p.Ser51Phe (c.152C>T) in the general population?

ABCE1 p.Ser51Phe (c.152C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ABCE1 p.Ser51Phe (c.152C>T)?

AlphaMissense predicts likely pathogenic (score 0.9663) — an in-silico prediction, not a clinical call.

ABCE1 p.Ser51Phe

c.152C>T · VCV3408903

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9663 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9663	likely pathogenic
REVEL	0.889	moderately pathogenic-leaning
SaProt	LLR -12.94	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.7, phastCons 1
Regional constraint	o/e 0.46	unconstrained · MANE · 23 kb · p 3.5e-48 · regional, not allelic
Overall
CADD	29.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

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: ABCE1
Protein: p.Ser51Phe
Coding: c.152C>T
MANE Select: NM_002940
Type: single nucleotide variant
Location: chr4:145105653 (GRCh38)
Gene constraint: LOEUF 0.466 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 86.76 · 3 PDB
Residue 51: the 4fe-4s ferredoxin-type 2 domain

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.Asp3Glu 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-ser51phe (accessed [today's date]).

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