MSRA

methionine sulfoxide reductase A

Basic information

Region (hg38): 8:10054291-10428891

Links

ENSG00000175806 ∙ NCBI:4482 ∙ OMIM:601250 ∙ HGNC:7377 ∙ Uniprot:Q9UJ68 ∙ 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 MSRA gene.

• Inborn genetic diseases (18 variants)
• MSRA-related condition (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

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

Variants in MSRA

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

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

Position	Type	Phenotype	Significance	ClinVar
8-10054520-C-G		not specified	Uncertain significance (Nov 09, 2023)
8-10054532-C-T		not specified	Uncertain significance (Nov 30, 2021)
8-10054539-C-T		not specified	Uncertain significance (Dec 19, 2022)
8-10054547-C-T		not specified	Uncertain significance (May 30, 2023)
8-10054556-C-T		not specified	Uncertain significance (Feb 16, 2023)
8-10054582-G-C		not specified	Uncertain significance (Jul 14, 2022)
8-10054634-C-G		not specified	Uncertain significance (Dec 28, 2022)
8-10054643-C-G		not specified	Uncertain significance (Sep 14, 2023)
8-10207815-CTT-C		MSRA-related disorder	Likely benign (May 22, 2019)
8-10207841-C-G		not specified	Uncertain significance (Dec 28, 2022)
8-10207874-C-T		not specified	Uncertain significance (Dec 11, 2023)
8-10207893-C-A		not specified	Uncertain significance (Dec 13, 2023)
8-10245133-A-C		not specified	Uncertain significance (Jan 09, 2024)
8-10245167-A-C		not specified	Uncertain significance (Apr 25, 2022)
8-10245168-A-G		MSRA-related disorder	Uncertain significance (Oct 03, 2022)
8-10245172-G-A			Likely benign (Apr 11, 2018)
8-10245191-C-G		not specified	Uncertain significance (Oct 04, 2022)
8-10301561-G-A		not specified	Uncertain significance (Apr 22, 2022)
8-10301574-G-C		not specified	Uncertain significance (Nov 21, 2023)
8-10301625-C-G		not specified	Uncertain significance (Sep 29, 2022)
8-10301626-G-C		not specified	Uncertain significance (Oct 13, 2023)
8-10319888-C-T		not specified	Uncertain significance (Oct 03, 2022)
8-10319942-G-A		not specified	Uncertain significance (Dec 15, 2023)
8-10428162-C-T		MSRA-related disorder	Likely benign (Dec 09, 2019)
8-10428179-C-G		not specified	Uncertain significance (May 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MSRA	protein_coding	protein_coding	ENST00000317173	6	374624

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.53e-15	0.000945	125566	0	182	125748	0.000724

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.63	221	135	1.64	0.00000733	1510
Missense in Polyphen		76	53.832	1.4118		610
Synonymous	-3.37	88	56.0	1.57	0.00000357	439
Loss of Function	-1.62	19	12.7	1.49	6.26e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00161	0.00154
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000937	0.0000924
European (Non-Finnish)	0.00131	0.00117
Middle Eastern	0.000109	0.000109
South Asian	0.000271	0.000261
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine.
• Pathway: Sulindac Metabolic Pathway;Methionine De Novo and Salvage Pathway;Metabolism of proteins;Protein repair (Consensus)

Recessive Scores

• pRec: 0.337

Intolerance Scores

• loftool: 0.169
• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.09

Haploinsufficiency Scores

• pHI: 0.0900
• hipred: N
• hipred_score: 0.318
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.507

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Msra
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: cellular protein modification process;methionine metabolic process;response to oxidative stress;protein repair;cellular response to oxidative stress;oxidation-reduction process
• Cellular component: nucleoplasm;cytoplasm;mitochondrion;cytosol;actin cytoskeleton;membrane;extracellular exosome
• Molecular function: peptide-methionine (S)-S-oxide reductase activity;L-methionine-(S)-S-oxide reductase activity