ARGLU1

arginine and glutamate rich 1

Basic information

Region (hg38): 13:106541673-106568137

Links

ENSG00000134884 ∙ NCBI:55082 ∙ OMIM:614046 ∙ HGNC:25482 ∙ Uniprot:Q9NWB6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARGLU1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARGLU1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			7		1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	1

Variants in ARGLU1

This is a list of pathogenic ClinVar variants found in the ARGLU1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
13-106543996-T-C		ARGLU1-related disorder	Likely benign (Aug 12, 2019)
13-106557121-C-T		not specified	Uncertain significance (Jun 10, 2024)
13-106559445-T-C		not specified	Uncertain significance (Aug 20, 2023)
13-106559449-C-T		ARGLU1-related disorder	Benign (Sep 05, 2019)
13-106559541-C-T		not specified	Uncertain significance (Feb 15, 2023)
13-106567693-G-A		not specified	Uncertain significance (Apr 20, 2024)
13-106567707-G-C		not specified	Uncertain significance (Aug 02, 2021)
13-106567723-G-T		not specified	Uncertain significance (May 24, 2024)
13-106567726-A-C		not specified	Uncertain significance (Feb 14, 2024)
13-106567733-T-G		not specified	Uncertain significance (Dec 01, 2022)
13-106567748-A-C		not specified	Uncertain significance (Nov 15, 2021)
13-106567821-G-C		not specified	Uncertain significance (Sep 13, 2023)
13-106567872-C-T		ARGLU1-related disorder	Likely benign (Mar 25, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARGLU1	protein_coding	protein_coding	ENST00000400198	4	26492

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.862	0.138	124782	0	3	124785	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.48	70	158	0.444	0.00000897	1752
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000201	0.000199
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000883	0.00000883
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.777
• hipred: Y
• hipred_score: 0.783
• ghis: 0.630

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arglu1

Gene ontology

• Cellular component: nucleoplasm;mitochondrion
• Molecular function: protein binding;cadherin binding