URM1

ubiquitin related modifier 1

Basic information

Region (hg38): 9:128371361-128392016

Previous symbols: [ "C9orf74" ]

Links

ENSG00000167118 ∙ NCBI:81605 ∙ OMIM:612693 ∙ HGNC:28378 ∙ Uniprot:Q9BTM9 ∙ 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 URM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the URM1 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						0
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8			8
Total	0	0	16	0	0

Variants in URM1

This is a list of pathogenic ClinVar variants found in the URM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128371385-C-T		not specified	Uncertain significance (Sep 12, 2023)
9-128378044-C-T		not specified	Uncertain significance (Sep 18, 2024)
9-128378046-G-C		not specified	Uncertain significance (Aug 27, 2024)
9-128378061-G-A		not specified	Uncertain significance (Sep 01, 2021)
9-128387816-G-T		not specified	Uncertain significance (Feb 23, 2023)
9-128387847-G-C		not specified	Uncertain significance (Aug 02, 2021)
9-128387867-G-A		not specified	Uncertain significance (Feb 15, 2023)
9-128387869-C-T		not specified	Uncertain significance (Jan 08, 2024)
9-128389277-G-T		not specified	Uncertain significance (Jan 21, 2025)
9-128389325-G-A		not specified	Uncertain significance (Mar 20, 2023)
9-128389326-A-G		not specified	Uncertain significance (Apr 20, 2023)
9-128389329-T-A		not specified	Uncertain significance (Mar 07, 2024)
9-128389413-C-T		not specified	Uncertain significance (Aug 10, 2023)
9-128389421-C-G		not specified	Uncertain significance (Jan 16, 2024)
9-128389429-C-G		not specified	Uncertain significance (Jul 31, 2024)
9-128389436-C-G		not specified	Uncertain significance (Jan 17, 2024)
9-128389475-A-C		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
URM1	protein_coding	protein_coding	ENST00000452446	4	19418

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0313	0.826	125737	0	8	125745	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.426	76	87.2	0.871	0.00000490	925
Missense in Polyphen		17	25.3	0.67194		270
Synonymous	-1.04	42	34.2	1.23	0.00000192	316
Loss of Function	1.14	3	6.03	0.497	3.22e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000444	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000701	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a sulfur carrier required for 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of cytosolic tRNA(Lys), tRNA(Glu) and tRNA(Gln). Serves as sulfur donor in tRNA 2- thiolation reaction by being thiocarboxylated (-COSH) at its C- terminus by MOCS3. The sulfur is then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U. Also acts as a ubiquitin-like protein (UBL) that is covalently conjugated via an isopeptide bond to lysine residues of target proteins such as MOCS3, ATPBD3, CTU2, USP15 and CAS. The thiocarboxylated form serves as substrate for conjugation and oxidative stress specifically induces the formation of UBL-protein conjugates. {ECO:0000255|HAMAP- Rule:MF_03048, ECO:0000269|PubMed:19017811, ECO:0000269|PubMed:21209336}.
• Pathway: Sulfur relay system - Homo sapiens (human);tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.298
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.296
• hipred: N
• hipred_score: 0.179
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Urm1

Gene ontology

• Biological process: tRNA wobble uridine modification;protein urmylation;tRNA thio-modification
• Cellular component: cytosol
• Molecular function: protein binding;sulfurtransferase activity