Is ETFB p.Ala45Glu (c.134C>A) pathogenic?

ETFB p.Ala45Glu (c.134C>A) is classified Uncertain significance in ETFB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-13). AlphaMissense: likely pathogenic (0.9922); Very rare (popmax 0.0033%, sas); Associated with Inborn genetic diseases.

What condition is associated with ETFB p.Ala45Glu (c.134C>A)?

ETFB p.Ala45Glu (c.134C>A) is associated with Inborn genetic diseases (ClinVar).

How common is ETFB p.Ala45Glu (c.134C>A) in the general population?

ETFB p.Ala45Glu (c.134C>A) is very rare (popmax 0.0033%, sas) (gnomAD).

What do computational predictors say about ETFB p.Ala45Glu (c.134C>A)?

AlphaMissense predicts likely pathogenic (score 0.9922) — an in-silico prediction, not a clinical call.

ETFB p.Ala45Glu

c.134C>A · VCV4618816

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9922 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0033%, sas)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9922	likely pathogenic · top 4% in ETFB
REVEL	0.971	strongly pathogenic-leaning
SaProt	LLR -13.66	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 11	GERP 1.4, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 21 kb · p 0.0022 · regional, not allelic
Overall
CADD	32.0	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

Grpmax group 0.0033% South Asian · 3/91,042 alleles

Filtering AF 0.000875% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000443%

Overall 0.00041% 6/1,461,864 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0033%	30,347
European (non-Finnish)	0.000254%	393,317

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: ETFB
Protein: p.Ala45Glu
Coding: c.134C>A
MANE Select: NM_001985
Type: single nucleotide variant
Location: chr19:51354232 (GRCh38)
Gene constraint: LOEUF 1.1 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.19 · 4 PDB
Residue 45: an α-helix

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ETFB p.Ala45Val Uncertain significance ★★ ⚠ same residue
ETFB p.Ala45= Likely benign ★★ same residue
ETFB p.Ala45Thr Uncertain significance ★ ⚠ same residue
ETFB p.Ala83Thr Uncertain significance ★★ ⚠ same condition
ETFB p.Arg174Cys Uncertain significance ★★ ⚠ same condition
ETFB p.Arg233Cys Uncertain significance ★★ ⚠ same condition
ETFB p.Arg254Gln Uncertain significance ★★ ⚠ same condition
ETFB p.Arg51Gln Uncertain significance ★★ ⚠ 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/etfb-p-ala45glu (accessed [today's date]).

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