Is ELMO2 p.Asp306Val (c.917A>T) pathogenic?

ELMO2 p.Asp306Val (c.917A>T) is classified Uncertain significance in ELMO2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-01). AlphaMissense: likely pathogenic (0.828); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ELMO2 p.Asp306Val (c.917A>T)?

ELMO2 p.Asp306Val (c.917A>T) is associated with Inborn genetic diseases (ClinVar).

How common is ELMO2 p.Asp306Val (c.917A>T) in the general population?

ELMO2 p.Asp306Val (c.917A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ELMO2 p.Asp306Val (c.917A>T)?

AlphaMissense predicts likely pathogenic (score 0.828) — an in-silico prediction, not a clinical call.

ELMO2 p.Asp306Val

c.917A>T · VCV4017563

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.828 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.828	likely pathogenic
REVEL	0.787	moderately pathogenic-leaning
SaProt	LLR -12.97	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 7.8	GERP 2.3, phastCons 1
Regional constraint	o/e 0.61	unconstrained · MANE · 27 kb · p 2.6e-31 · 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

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: ELMO2
Protein: p.Asp306Val
Coding: c.917A>T
MANE Select: NM_133171
Type: single nucleotide variant
Location: chr20:46375681 (GRCh38)
Gene constraint: LOEUF 0.486 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 88.96 · 2 PDB

Full ELMO2 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

ELMO2 p.Asn490Lys Uncertain significance ★★ ⚠ same condition
ELMO2 p.Glu468Asp Uncertain significance ★★ ⚠ same condition
ELMO2 p.Ser396Gly Uncertain significance ★★ ⚠ same condition
ELMO2 p.Thr482Ala Uncertain significance ★★ ⚠ same condition
ELMO2 p.Ala235Thr Uncertain significance ★ ⚠ same condition
ELMO2 p.Ala246Ser Uncertain significance ★ ⚠ same condition
ELMO2 p.Ala333Gly Uncertain significance ★ ⚠ same condition
ELMO2 p.Ala467Thr 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/elmo2-p-asp306val (accessed [today's date]).

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