MSN

moesin, the group of FERM domain containing

Basic information

Region (hg38): X:65588377-65741931

Links

ENSG00000147065 ∙ NCBI:4478 ∙ OMIM:309845 ∙ HGNC:7373 ∙ Uniprot:P26038 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined immunodeficiency due to moesin deficiency (Supportive), mode of inheritance: XL
• combined immunodeficiency due to moesin deficiency (Strong), mode of inheritance: XL
• combined immunodeficiency due to moesin deficiency (Moderate), mode of inheritance: XL
• combined immunodeficiency due to moesin deficiency (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 50	XL	Allergy/Immunology/Infectious	Individuals have been described with early onset and recurrent bacterial or varicella zoster virus infections, and awareness may allow preventive measures and early and aggressive treatments of infections	Allergy/Immunology/Infectious	27405666

ClinVar

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

• not provided (1 variants)
• Combined immunodeficiency due to moesin deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSN 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				42	11	53
missense	1	1	69	6	8	85
nonsense		1	6			7
start loss						0
frameshift			3			3
inframe indel			2			2
splice donor/acceptor (+/-2bp)			1			1
splice region			3	10	4	17
non coding			1	18	5	24
Total	1	2	82	66	24

Variants in MSN

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

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

Position	Type	Phenotype	Significance	ClinVar
X-65667862-CG-C			Likely benign (Apr 23, 2022)
X-65667863-G-A			Likely benign (Jun 20, 2023)
X-65667870-G-GC			Likely benign (Nov 28, 2022)
X-65716808-C-A			Likely benign (Dec 30, 2022)
X-65716813-C-A			Uncertain significance (Sep 01, 2023)
X-65716817-G-A			Uncertain significance (Apr 24, 2022)
X-65716827-C-T			Uncertain significance (Dec 11, 2023)
X-65716828-G-A			Likely benign (Oct 10, 2022)
X-65716854-G-T			Uncertain significance (Jul 16, 2022)
X-65716855-A-C			Uncertain significance (Aug 31, 2018)
X-65716863-A-G		Inborn genetic diseases	Uncertain significance (Jul 26, 2022)
X-65716865-C-T			Likely benign (Sep 21, 2022)
X-65716868-G-T			Uncertain significance (Oct 03, 2023)
X-65716873-A-G			Uncertain significance (Apr 02, 2022)
X-65716880-C-G			Likely benign (Jul 04, 2023)
X-65716883-G-A			Likely benign (May 12, 2022)
X-65716898-C-T			Likely benign (Jun 30, 2022)
X-65716908-C-T		MSN-related disorder	Benign/Likely benign (Jan 31, 2024)
X-65716909-G-A			Likely benign (Nov 27, 2023)
X-65727826-A-G			Uncertain significance (Dec 07, 2022)
X-65727833-T-A			Uncertain significance (Sep 08, 2023)
X-65727839-A-G		Inborn genetic diseases	Uncertain significance (May 27, 2022)
X-65727840-A-G			Likely benign (Jul 29, 2023)
X-65727856-C-A		Autism	Uncertain significance (-)
X-65727861-G-C		Inborn genetic diseases	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MSN	protein_coding	protein_coding	ENST00000360270	13	153535

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000331	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.93	110	237	0.464	0.0000200	3830
Missense in Polyphen		22	90.523	0.24303		1517
Synonymous	0.0771	82	82.9	0.989	0.00000619	1030
Loss of Function	4.44	0	23.0	0.00	0.00000173	386

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably involved in connections of major cytoskeletal structures to the plasma membrane. May inhibit herpes simplex virus 1 infection at an early stage. Plays a role in regulating the proliferation, migration, and adhesion of human lymphoid cells and participates in immunologic synapse formation (PubMed:27405666). {ECO:0000269|PubMed:21549406, ECO:0000269|PubMed:27405666}.
• Disease: DISEASE: Immunodeficiency 50 (IMD50) [MIM:300988]: A primary immunodeficiency disorder characterized by onset of recurrent bacterial or varicella zoster virus infections in early childhood, profound lymphopenia, hypogammaglobulinemia, fluctuating monocytopenia and neutropenia, and a poor immune response to vaccine antigens. {ECO:0000269|PubMed:27405666}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Tight junction - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Measles - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Glial Cell Differentiation;AGE-RAGE pathway;Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;Regulation of Actin Cytoskeleton;Developmental Biology;RAGE;Recycling pathway of L1;KitReceptor;L1CAM interactions;Axon guidance;Plasma membrane estrogen receptor signaling;RhoA signaling pathway (Consensus)

Recessive Scores

• pRec: 0.453

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.863
• hipred: Y
• hipred_score: 0.825
• ghis: 0.626

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Msn
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: msna
• Affected structure: blood vessel endothelial cell
• Phenotype tag: abnormal
• Phenotype quality: physical object quality

Gene ontology

• Biological process: immunological synapse formation;cytoskeleton organization;leukocyte cell-cell adhesion;regulation of cell shape;regulation of cell size;positive regulation of gene expression;gland morphogenesis;membrane to membrane docking;interleukin-12-mediated signaling pathway;T cell proliferation;establishment of epithelial cell apical/basal polarity;leukocyte migration;establishment of endothelial barrier;T cell aggregation;cellular response to testosterone stimulus;positive regulation of podosome assembly;T cell migration;regulation of organelle assembly;positive regulation of protein localization to early endosome;positive regulation of cellular protein catabolic process;regulation of lymphocyte migration;positive regulation of early endosome to late endosome transport
• Cellular component: uropod;extracellular space;nucleus;cytoplasm;cytosol;cytoskeleton;plasma membrane;microvillus;focal adhesion;cell surface;basolateral plasma membrane;apical plasma membrane;filopodium;pseudopodium;microvillus membrane;vesicle;myelin sheath;apical part of cell;perinuclear region of cytoplasm;extracellular exosome;invadopodium;cell periphery;blood microparticle
• Molecular function: double-stranded RNA binding;actin binding;signaling receptor binding;structural constituent of cytoskeleton;protein binding;enzyme binding;protein kinase binding;cell adhesion molecule binding