MRI1

methylthioribose-1-phosphate isomerase 1

Basic information

Region (hg38): 19:13764521-13774282

Links

ENSG00000037757 ∙ NCBI:84245 ∙ OMIM:615105 ∙ HGNC:28469 ∙ Uniprot:Q9BV20 ∙ 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 MRI1 gene.

• Inborn genetic diseases (22 variants)
• not provided (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRI1 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				3	1	4
missense			23	2	2	27
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding				5	2	7
Total	0	0	25	10	5

Variants in MRI1

This is a list of pathogenic ClinVar variants found in the MRI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-13764607-C-T			Benign (Dec 31, 2019)
19-13764620-G-A		not specified	Uncertain significance (Aug 12, 2022)
19-13764665-G-A		not specified	Uncertain significance (Apr 20, 2023)
19-13764725-AGCGGGGCG-A			Likely benign (Jan 23, 2024)
19-13764725-AGCGGGGCGGCGGGGCGGCGGGGCG-A			Likely benign (Jan 18, 2024)
19-13764725-AGCGGGGCGGCGGGGCGGCGGGGCGGCGGGGCG-A			Likely benign (Oct 11, 2023)
19-13764725-AGCGGGGCGGCGGGGCGGCGGGGCGGCGGGGCGGCGGGGCG-A			Likely benign (Jan 23, 2024)
19-13764725-A-AGCGGGGCG			Benign (Jan 18, 2024)
19-13764892-G-T		not specified	Uncertain significance (Feb 13, 2023)
19-13764950-G-A		not specified	Uncertain significance (Mar 01, 2024)
19-13764977-G-T		not specified	Uncertain significance (Feb 02, 2024)
19-13765024-A-G		not specified	Uncertain significance (Aug 10, 2021)
19-13765028-C-G		not specified	Uncertain significance (Jan 19, 2022)
19-13765041-C-T			Likely benign (Jun 25, 2018)
19-13765063-C-T		not specified	Uncertain significance (Dec 21, 2022)
19-13765090-G-A			Likely benign (Dec 31, 2019)
19-13765097-CGGTCCGGGAGA-C			Uncertain significance (Sep 29, 2019)
19-13766021-G-C		not specified	Uncertain significance (Aug 12, 2022)
19-13766035-C-G			Likely benign (Jun 16, 2018)
19-13766042-C-G		not specified	Uncertain significance (Feb 14, 2024)
19-13766042-C-T		not specified	Uncertain significance (May 26, 2022)
19-13766049-C-T		not specified	Uncertain significance (Dec 16, 2022)
19-13766056-C-T			Likely benign (Apr 23, 2018)
19-13766064-A-C		not specified	Uncertain significance (Aug 12, 2021)
19-13766108-G-A		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRI1	protein_coding	protein_coding	ENST00000040663	6	9751

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000406	0.863	125692	0	51	125743	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.348	203	217	0.934	0.0000127	2292
Missense in Polyphen		98	94.103	1.0414		980
Synonymous	0.367	93	97.6	0.953	0.00000577	847
Loss of Function	1.32	7	11.9	0.587	6.77e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000707	0.000706
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000473	0.0000462
European (Non-Finnish)	0.000206	0.000202
Middle Eastern	0.00	0.00
South Asian	0.0000655	0.0000653
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the interconversion of methylthioribose-1- phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1- P). Independently from catalytic activity, promotes cell invasion in response to constitutive RhoA activation by promoting FAK tyrosine phosphorylation and stress fiber turnover. {ECO:0000255|HAMAP-Rule:MF_03119, ECO:0000269|PubMed:19620624}.
• Pathway: Cysteine and methionine metabolism - Homo sapiens (human);Methionine De Novo and Salvage Pathway;Metabolism of polyamines;Metabolism of amino acids and derivatives;Methionine salvage pathway;Metabolism;<i>S</i>-methyl-5-thio-&alpha;-D-ribose 1-phosphate degradation;<i>S</i>-methyl-5-thio-&alpha;-D-ribose 1-phosphate degradation;methionine salvage cycle III;Sulfur amino acid metabolism (Consensus)

Intolerance Scores

• loftool: 0.194
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.2

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0654

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mri1

Gene ontology

• Biological process: L-methionine salvage from S-adenosylmethionine;L-methionine salvage from methylthioadenosine
• Cellular component: fibrillar center;nucleoplasm;cytosol;cell projection
• Molecular function: identical protein binding;S-methyl-5-thioribose-1-phosphate isomerase activity