Is ELAC2 p.Pro300del (c.894TCC[1]) pathogenic?

ELAC2 p.Pro300del (c.894TCC[1]) is classified Likely pathogenic in ELAC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-02-22). Absent from gnomAD.

How common is ELAC2 p.Pro300del (c.894TCC[1]) in the general population?

ELAC2 p.Pro300del (c.894TCC[1]) is absent from gnomAD (gnomAD).

ELAC2 p.Pro300del

c.894TCC[1] · rs1064796732 · VCV423989

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -3.8	GERP -4.2

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ELAC2
Protein: p.Pro300del
Coding: c.894TCC[1]
MANE Select: NM_018127
dbSNP: rs1064796732
Type: Microsatellite
Location: chr17:13005073 (GRCh38)
Gene constraint: LOEUF 1.02 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.81 · 10 PDB
Residue 300: an α-helix

Full ELAC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ELAC2 p.Pro300Ser Uncertain significance ★ ⚠ same residue
ELAC2 p.Pro300= Likely benign ★ same residue
ELAC2 p.Arg477del Uncertain significance ★★ same type
ELAC2 c.2253+14_2253+15del Likely benign ★★ same type
ELAC2 p.Glu290fs Pathogenic ★ same type
ELAC2 p.Gly288fs Pathogenic ★ same type
ELAC2 p.Arg465del Uncertain significance ★ same type
ELAC2 p.Arg824fs 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/elac2-p-pro300del (accessed [today's date]).

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