MSR1

macrophage scavenger receptor 1, the group of CD molecules|Scavenger receptor cysteine rich domain containing|Scavenger receptors

Basic information

Region (hg38): 8:16107877-16567490

Links

ENSG00000038945 ∙ ∙ OMIM:153622 ∙ HGNC:7376 ∙ Uniprot:P21757 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Barrett esophagus (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Barrett esophagus/esophageal adenocarcinoma; Prostate cancer	AD	Gastrointestinal; Oncologic	Awareness of disease risk may allow surveillance, preventive measures (eg, related to Barrett esophagus) and early treatment of malignancy, which may reduce morbidity and mortality	Gastrointestinal; Oncologic	11443539; 12244320; 12839931; 12958598; 15536476; 16287155; 17768178; 17903305; 18398045; 20086112; 21791690
While some (eg, common) variants may increase the risk of prostate cancer slightly, others appear to confer much higher risk

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MSR1 gene.

• Inborn genetic diseases (29 variants)
• not provided (15 variants)
• Ovarian cancer (8 variants)
• Malignant tumor of prostate (2 variants)
• Barrett esophagus (2 variants)
• X-linked Alport syndrome (1 variants)
• Hereditary cancer-predisposing syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSR1 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	4	5
missense		5	29	2	4	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	1	1		1		3
splice region				1	1	2
non coding				2	1	3
Total	1	6	29	6	9

Highest pathogenic variant AF is 0.0000526

Variants in MSR1

This is a list of pathogenic ClinVar variants found in the MSR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-16110107-G-C		not specified	Uncertain significance (Jul 12, 2023)
8-16110129-C-G		not specified	Uncertain significance (Nov 30, 2022)
8-16110147-G-A		not specified	Uncertain significance (Sep 20, 2023)
8-16110218-C-G		Ovarian cancer	Likely pathogenic (Jan 01, 2022)
8-16120421-G-C		not specified	Uncertain significance (May 05, 2023)
8-16120435-G-A		not specified	Uncertain significance (Dec 27, 2022)
8-16120446-G-A			Benign (Jul 14, 2017)
8-16120484-C-T		not specified	Uncertain significance (Dec 05, 2022)
8-16120489-C-A		not specified	Uncertain significance (Oct 26, 2022)
8-16120512-G-A			Benign (Feb 26, 2018)
8-16120516-C-T		not specified	Uncertain significance (Feb 16, 2023)
8-16120554-C-T		MSR1-related disorder	Benign (Nov 26, 2019)
8-16120558-C-G		not specified	Uncertain significance (Nov 21, 2022)
8-16120602-T-C		MSR1-related disorder	Benign (Jul 10, 2019)
8-16120614-G-T			Likely benign (Dec 31, 2019)
8-16120615-TTAAAAA-T			Likely benign (Dec 31, 2019)
8-16120615-TTAAAAAAA-T		MSR1-related disorder	Benign (Oct 31, 2019)
8-16120615-TTAAAAAAAAA-T			Likely benign (May 05, 2021)
8-16120616-TA-T			Benign (Jan 12, 2024)
8-16143548-A-G			Benign (Feb 26, 2018)
8-16143557-C-G			Pathogenic (Jun 27, 2017)
8-16143577-C-T			Benign (Aug 15, 2018)
8-16150284-C-T		not specified	Uncertain significance (Jul 17, 2023)
8-16150291-C-A			Uncertain significance (-)
8-16150297-T-C		not specified	Uncertain significance (Aug 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MSR1	protein_coding	protein_coding	ENST00000262101	9	459613

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.16e-20	0.000248	125632	0	116	125748	0.000461

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.07	341	249	1.37	0.0000134	2955
Missense in Polyphen		99	75.614	1.3093		944
Synonymous	-1.43	105	87.9	1.19	0.00000497	838
Loss of Function	-1.05	27	21.7	1.24	0.00000105	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00308	0.00308
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000942	0.0000924
European (Non-Finnish)	0.000283	0.000281
Middle Eastern	0.000218	0.000217
South Asian	0.000100	0.0000980
Other	0.000984	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Membrane glycoproteins implicated in the pathologic deposition of cholesterol in arterial walls during atherogenesis. Two types of receptor subunits exist. These receptors mediate the endocytosis of a diverse group of macromolecules, including modified low density lipoproteins (LDL) (PubMed:2251254). Isoform III does not internalize acetylated LDL (PubMed:9548586). {ECO:0000269|PubMed:2251254, ECO:0000269|PubMed:9548586}.
• Disease: DISEASE: Barrett esophagus (BE) [MIM:614266]: A condition characterized by a metaplastic change in which normal esophageal squamous epithelium is replaced by a columnar and intestinal-type epithelium. Patients with Barrett esophagus have an increased risk of esophageal adenocarcinoma. The main cause of Barrett esophagus is gastroesophageal reflux. The retrograde movement of acid and bile salts from the stomach into the esophagus causes prolonged injury to the esophageal epithelium and induces chronic esophagitis, which in turn is believed to trigger the pathologic changes. {ECO:0000269|PubMed:21791690}. Note=The disease may be caused by mutations affecting the gene represented in this entry. Genetic variants in MSR1 have been found in individuals with Barrett esophagus and are thought to contribute to disease susceptibility.
• Pathway: Phagosome - Homo sapiens (human);AGE-RAGE pathway;Vesicle-mediated transport;Binding and Uptake of Ligands by Scavenger Receptors;Scavenging by Class A Receptors (Consensus)

Recessive Scores

• pRec: 0.0964

Intolerance Scores

• loftool: 0.106
• rvis_EVS: 0
• rvis_percentile_EVS: 54.03

Haploinsufficiency Scores

• pHI: 0.586
• hipred: N
• hipred_score: 0.146
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.778

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Msr1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: receptor-mediated endocytosis;phagocytosis, engulfment;negative regulation of gene expression;positive regulation of macrophage derived foam cell differentiation;positive regulation of cholesterol storage;cholesterol transport;plasma lipoprotein particle clearance;lipoprotein transport;amyloid-beta clearance
• Cellular component: collagen trimer;plasma membrane;integral component of plasma membrane;integral component of membrane;endocytic vesicle membrane;low-density lipoprotein particle
• Molecular function: amyloid-beta binding;scavenger receptor activity;protein binding;low-density lipoprotein particle binding