Is ELMO2 p.Glu90= (c.270G>A) pathogenic?

ELMO2 p.Glu90= (c.270G>A) is classified Likely benign in ELMO2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-01). Very rare (popmax 6.2e-05%).

How common is ELMO2 p.Glu90= (c.270G>A) in the general population?

ELMO2 p.Glu90= (c.270G>A) is very rare (popmax 6.2e-05%) (gnomAD).

ELMO2 p.Glu90=

c.270G>A · rs2516222985 · VCV2652370

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 6.2e-05%)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.24	GERP -0.16, phastCons 0.25
Overall
CADD	7.463	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.2e-05%

Overall 6.2e-05% 1/1,614,120 alleles · very rare exomes 1/1,461,802 · genomes 0/152,318 · joint denominator

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: ELMO2
Protein: p.Glu90=
Coding: c.270G>A
MANE Select: NM_133171
dbSNP: rs2516222985
Type: single nucleotide variant
Location: chr20:46389194 (GRCh38)
Gene constraint: LOEUF 0.486 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 88.96 · 2 PDB
Residue 90: an α-helix

Full ELMO2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ELMO2 p.Arg478Gln Uncertain significance ★★ ⚠ same type
ELMO2 p.Asn490Lys Uncertain significance ★★ ⚠ same type
ELMO2 p.Glu468Asp Uncertain significance ★★ ⚠ same type
ELMO2 p.Ser396Gly Uncertain significance ★★ ⚠ same type
ELMO2 p.Thr482Ala Uncertain significance ★★ ⚠ same type
ELMO2 c.1065+87A>G Benign ★★ same type
ELMO2 c.1066-47T>C Benign ★★ same type
ELMO2 c.1580+23C>G Benign ★★ 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/elmo2-p-glu90 (accessed [today's date]).

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