Is EFCAB5 p.Ser552Ala (c.1654T>G) pathogenic?

EFCAB5 p.Ser552Ala (c.1654T>G) is classified Uncertain significance in EFCAB5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-20). AlphaMissense: likely benign (0.0773); Absent from gnomAD v4.1.

How common is EFCAB5 p.Ser552Ala (c.1654T>G) in the general population?

EFCAB5 p.Ser552Ala (c.1654T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EFCAB5 p.Ser552Ala (c.1654T>G)?

AlphaMissense predicts likely benign (score 0.0773) — an in-silico prediction, not a clinical call.

EFCAB5 p.Ser552Ala

c.1654T>G · VCV4246927

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0773 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0773	likely benign
REVEL	0.016	strongly benign-leaning
SaProt	LLR -9.05	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.61	GERP -0.74, phastCons 0.002
Regional constraint	o/e 0.95	unconstrained · MANE · 166 kb · p 0.049 · regional, not allelic
Overall
CADD	9.892	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

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: EFCAB5
Protein: p.Ser552Ala
Coding: c.1654T>G
MANE Select: NM_198529
Type: single nucleotide variant
Location: chr17:30053608 (GRCh38)
Gene constraint: LOEUF 0.908 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.22
Residue 552: the 'disordered' region

Full EFCAB5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EFCAB5 p.Ala1262Pro Uncertain significance ★ same type
EFCAB5 p.Ala128Thr Uncertain significance ★ ⚠ same type
EFCAB5 p.Ala1493Val Uncertain significance ★ ⚠ same type
EFCAB5 p.Ala373Val Uncertain significance ★ ⚠ same type
EFCAB5 p.Ala514Thr Uncertain significance ★ ⚠ same type
EFCAB5 p.Ala5Pro Uncertain significance ★ ⚠ same type
EFCAB5 p.Arg1158Gln Uncertain significance ★ ⚠ same type
EFCAB5 p.Arg1329Gln 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/efcab5-p-ser552ala (accessed [today's date]).

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