ARGLU1

protein-coding

arginine and glutamate rich 1

Gene summary

Enables pre-mRNA binding activity and transcription coactivator activity. Involved in regulation of alternative mRNA splicing, via spliceosome. Located in nuclear speck. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_018011.4

Inheritance

—

ClinVar variants

U:17B:3

Top phenotype

ARGLU1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr13:106,541,673-106,568,137

External References & Databases

Ensembl (ENSG00000134884)

Transcript & Mutation Effects

hg38 • Region Span ~26.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ARGLU1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 16

ARGLU1-related disorderTotal: 3

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018011.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			16 clinvar		1 clinvar	17
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	17	2	1	20

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018011.4	RefSeq	NP_060481.3	4	MANE Select
ENST00000400198.8	Ensembl	ENSP00000383059.3	4	MANE Select
ENST00000868085.1	Ensembl	ENSP00000538144.1	4	Standard
ENST00000868085.2	Ensembl	ENSP00000538144.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
cadherin binding

Cellular Component

nucleoplasm
mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000400198
Coding exons: 4
Length: 26492
Individuals with no LoFs: 124782
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 124785
p: 0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.48	70	158	0.444	0.00000897	1752
Missense (PolyPhen)		1	3.1848	0.31399		34
Synonymous	-0.802	72	63.8	1.13	0.00000313	543
Loss of Function	3.48	3	19.7	0.152	0.00000154	160

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for the estrogen-dependent expression of ESR1 target genes. Can act in cooperation with MED1. {ECO:0000269|PubMed:21454576}.;

Recessive Scores

pRec: 0.0683

Intolerance Scores

LoFtool: 0.0676
RVIS EVS: -0.1
RVIS percentile EVS: 46.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.903

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Low	Low	Low