Is ELMO3 p.Ser146Arg (c.438C>A) pathogenic?

ELMO3 p.Ser146Arg (c.438C>A) is classified Uncertain significance in ELMO3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-09). AlphaMissense: likely pathogenic (0.9167); Very rare (popmax 0.00667%, amr).

How common is ELMO3 p.Ser146Arg (c.438C>A) in the general population?

ELMO3 p.Ser146Arg (c.438C>A) is very rare (popmax 0.00667%, amr) (gnomAD).

What do computational predictors say about ELMO3 p.Ser146Arg (c.438C>A)?

AlphaMissense predicts likely pathogenic (score 0.9167) — an in-silico prediction, not a clinical call.

ELMO3 p.Ser146Arg

c.438C>A · VCV4017581

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9167 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00667%, amr)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9167	likely pathogenic
REVEL	0.085	moderately benign-leaning
SaProt	LLR -12.60	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.39	GERP -3.8, phastCons 0.29
Regional constraint	o/e 0.99	unconstrained · MANE · 4,547 bp · p 0.66 · regional, not allelic
Overall
CADD	11.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00667% Admixed American · 4/59,988 alleles

Filtering AF 0.00226% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00135%

Overall 0.000434% 7/1,613,348 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00667%	14,997
European (non-Finnish)	0.000254%	393,258

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: ELMO3
Protein: p.Ser146Arg
Coding: c.438C>A
MANE Select: NM_024712
Type: single nucleotide variant
Location: chr16:67200475 (GRCh38)
Gene constraint: LOEUF 1.093 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.04

Full ELMO3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ELMO3 p.Val284Ile Likely benign ★★ same type
ELMO3 c.1780+1G>A Uncertain significance ★ same type
ELMO3 c.-11C>T Uncertain significance ★ same type
ELMO3 c.-123A>G Uncertain significance ★ same type
ELMO3 c.-14G>T Uncertain significance ★ same type
ELMO3 c.-28G>C Uncertain significance ★ same type
ELMO3 c.-50G>A Uncertain significance ★ same type
ELMO3 c.-77G>A 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/elmo3-p-ser146arg (accessed [today's date]).

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