Is EMB p.Arg145Gln (c.434G>A) pathogenic?

EMB p.Arg145Gln (c.434G>A) is classified Likely benign in EMB (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-07). AlphaMissense: likely benign (0.0649); Very rare (popmax 0.00898%, sas).

How common is EMB p.Arg145Gln (c.434G>A) in the general population?

EMB p.Arg145Gln (c.434G>A) is very rare (popmax 0.00898%, sas) (gnomAD).

What do computational predictors say about EMB p.Arg145Gln (c.434G>A)?

AlphaMissense predicts likely benign (score 0.0649) — an in-silico prediction, not a clinical call.

EMB p.Arg145Gln

c.434G>A · VCV3508134

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0649 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00898%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0649	likely benign
REVEL	0.014	strongly benign-leaning
SaProt	LLR -5.74	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.56 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.098	GERP -2.3
Overall
CADD	3.255	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 0.00898% South Asian · 8/89,114 alleles

Filtering AF 0.00445% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00318%

Overall 0.00305% 49/1,605,078 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00898%	11,139
Remaining individualsnot grpmax-eligible	0.00645%	15,511
East Asian	0.0045%	22,238
Admixed American	0.00343%	29,159
European (non-Finnish)	0.0028%	35,657

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: EMB
Protein: p.Arg145Gln
Coding: c.434G>A
MANE Select: NM_003400 · reported on NM_198449
Type: single nucleotide variant
Location: chr5:50410915 (GRCh38)
Structure: AlphaFold pLDDT 91.62 · 19 PDB
Residue 145: the 'necessary for htlv-1 rex-mediated mrna export' region; an α-helix

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

Similar variants

XPO1 c.888+9A>G Benign ★★ same type
XPO1 p.Arg305= Benign ★★ same type
XPO1 p.Leu625= Likely benign ★★ same type
XPO1 p.Lys757= Likely benign ★★ same type
XPO1 p.Thr846= Benign ★★ same type
XPO1 c.1887+1G>T Pathogenic ★ same type
XPO1 c.888+1G>A Pathogenic ★ same type
XPO1 p.Arg765Ter Pathogenic ★ 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/emb-p-arg145gln (accessed [today's date]).

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