MR1

major histocompatibility complex, class I-related, the group of C1-set domain containing|Minor histocompatibility antigens

Basic information

Region (hg38): 1:181033374-181061938

Previous symbols: [ "HLALS" ]

Links

ENSG00000153029 ∙ NCBI:3140 ∙ OMIM:600764 ∙ HGNC:4975 ∙ Uniprot:Q95460 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Paroxysmal nonkinesigenic dyskinesia 1	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	8659518; 9490305; 15496428; 15262732; 15824259; 16216955; 17515540; 19124534; 22967746
Medical treatment (eg, with benzodiazepines) have been described as beneficial

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MR1 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			1		1	2
missense			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	1

Variants in MR1

This is a list of pathogenic ClinVar variants found in the MR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-181034045-T-C		not specified	Uncertain significance (Jun 18, 2021)
1-181034047-G-A		not specified	Uncertain significance (May 24, 2023)
1-181049076-G-A		Immunodeficiency	Likely benign (Oct 01, 2024)
1-181049084-G-A		not specified	Likely benign (Dec 28, 2023)
1-181049100-A-G		not specified	Benign (-)
1-181049117-A-G		not specified	Uncertain significance (May 21, 2024)
1-181049122-G-A		not specified	Benign (-)
1-181049123-G-A		not specified	Uncertain significance (Mar 30, 2022)
1-181049132-G-A		not specified	Uncertain significance (Jun 22, 2021)
1-181049146-T-C			Benign (May 09, 2018)
1-181049186-C-T		not specified	Uncertain significance (Apr 26, 2024)
1-181049247-T-C		not specified	Uncertain significance (Sep 01, 2021)
1-181049257-G-C		not specified	Uncertain significance (Aug 15, 2023)
1-181049307-A-T		not specified	Uncertain significance (Sep 27, 2021)
1-181050019-A-G		not specified	Uncertain significance (Nov 21, 2023)
1-181050022-T-C		not specified	Uncertain significance (Sep 22, 2023)
1-181050062-G-A		not specified	Uncertain significance (Oct 13, 2015)
1-181050067-A-G		not specified	Uncertain significance (Dec 06, 2021)
1-181050091-G-A		not specified	Uncertain significance (May 14, 2024)
1-181050092-A-G		not specified	Uncertain significance (Aug 10, 2021)
1-181050116-A-G		not specified	Uncertain significance (Jul 12, 2023)
1-181050169-C-G		not specified	Uncertain significance (Apr 26, 2024)
1-181050218-T-C		not specified	Uncertain significance (Mar 19, 2024)
1-181052416-G-A			Uncertain significance (Nov 17, 2015)
1-181052426-A-G		not specified	Likely benign (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MR1	protein_coding	protein_coding	ENST00000367580	6	28008

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.90e-18	0.000441	125642	0	106	125748	0.000422

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.343	205	192	1.07	0.0000103	2222
Missense in Polyphen		79	73.035	1.0817		918
Synonymous	-0.124	76	74.6	1.02	0.00000422	660
Loss of Function	-1.33	23	17.1	1.35	7.98e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000490	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.000490	0.000489
South Asian	0.00229	0.00229
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Antigen-presenting molecule specialized in presenting microbial vitamin B metabolites. Involved in the development and expansion of a small population of T-cells expressing an invariant T-cell receptor alpha chain called mucosal-associated invariant T- cells (MAIT). MAIT lymphocytes are preferentially located in the gut lamina propria and therefore may be involved in monitoring commensal flora or serve as a distress signal. Expression and MAIT cell recognition seem to be ligand-dependent. {ECO:0000269|PubMed:12794138, ECO:0000269|PubMed:19416870}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.818
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.38

Haploinsufficiency Scores

• pHI: 0.0825
• hipred: N
• hipred_score: 0.170
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.123

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mr1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: cytokine production involved in immune response;antigen processing and presentation of peptide antigen via MHC class I;immune response;interleukin-1 beta production;interleukin-17 production;innate immune response;defense response to Gram-negative bacterium
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;external side of plasma membrane;integral component of membrane;MHC class I protein complex
• Molecular function: protein binding;MHC class I receptor activity