MSRB1

methionine sulfoxide reductase B1, the group of Selenoproteins

Basic information

Region (hg38): 16:1938229-1943199

Previous symbols: [ "SEPX1" ]

Links

ENSG00000198736 ∙ NCBI:51734 ∙ OMIM:606216 ∙ HGNC:14133 ∙ Uniprot:Q9NZV6 ∙ 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 MSRB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSRB1 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
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	0

Variants in MSRB1

This is a list of pathogenic ClinVar variants found in the MSRB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1940790-A-G		not specified	Uncertain significance (Apr 19, 2024)
16-1940831-G-A		not specified	Uncertain significance (Jan 08, 2024)
16-1940892-C-T		not specified	Uncertain significance (Jul 13, 2022)
16-1941274-T-C		not specified	Uncertain significance (Jan 03, 2024)
16-1941288-C-T		not specified	Uncertain significance (May 13, 2024)
16-1941291-T-C		not specified	Uncertain significance (Jun 17, 2024)
16-1941326-C-T			Likely benign (Jul 31, 2018)
16-1941342-G-A		not specified	Uncertain significance (Dec 09, 2023)
16-1941403-C-T		not specified	Likely benign (Apr 25, 2022)
16-1943116-T-C		not specified	Uncertain significance (Nov 17, 2023)
16-1943135-C-G		not specified	Uncertain significance (Aug 02, 2023)
16-1943143-C-G		not specified	Uncertain significance (May 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MSRB1	protein_coding	protein_coding	ENST00000361871	4	5117

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.130	0.788	124707	0	14	124721	0.0000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.118	80	77.1	1.04	0.00000496	763
Missense in Polyphen		19	22.083	0.86037		263
Synonymous	0.231	34	35.8	0.951	0.00000292	210
Loss of Function	1.40	2	5.56	0.360	2.35e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000978	0.0000972
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Methionine-sulfoxide reductase that specifically reduces methionine (R)-sulfoxide back to methionine. While in many cases, methionine oxidation is the result of random oxidation following oxidative stress, methionine oxidation is also a post- translational modification that takes place on specific residue. Acts as a regulator of actin assembly by reducing methionine (R)- sulfoxide mediated by MICALs (MICAL1, MICAL2 or MICAL3) on actin, thereby promoting filament repolymerization. Plays a role in innate immunity by reducing oxidized actin, leading to actin repolymerization in macrophages. {ECO:0000250|UniProtKB:Q9JLC3}.
• Pathway: Selenium Micronutrient Network;Selenium Metabolism and Selenoproteins;Metabolism of proteins;Protein repair (Consensus)

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.26

Haploinsufficiency Scores

• pHI: 0.0891
• hipred: N
• hipred_score: 0.231
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Msrb1
• Phenotype: cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: response to oxidative stress;actin filament polymerization;protein repair;innate immune response;oxidation-reduction process
• Cellular component: cellular_component;nucleus;cytosol;actin cytoskeleton
• Molecular function: actin binding;zinc ion binding;peptide-methionine (R)-S-oxide reductase activity;L-methionine-(R)-S-oxide reductase activity;methionine-R-sulfoxide reductase activity