MSLN

mesothelin

Basic information

Region (hg38): 16:760734-768865

Links

ENSG00000102854 ∙ NCBI:10232 ∙ OMIM:601051 ∙ HGNC:7371 ∙ Uniprot:Q13421 ∙ 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 MSLN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSLN 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	2	3
missense			64	7	6	77
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding				1	2	3
Total	0	0	64	9	10

Variants in MSLN

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

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

Position	Type	Phenotype	Significance	ClinVar
16-762702-C-A		not specified	Uncertain significance (Jun 22, 2024)
16-762729-G-A		not specified	Likely benign (Mar 29, 2022)
16-763244-C-T		not specified	Uncertain significance (Jan 30, 2024)
16-763260-C-T		not specified	Uncertain significance (Feb 06, 2024)
16-763649-C-T		not specified	Uncertain significance (Apr 17, 2023)
16-764069-G-A		not specified	Uncertain significance (Oct 06, 2021)
16-764079-C-T		not specified	Uncertain significance (Dec 27, 2023)
16-764081-G-A		not specified	Uncertain significance (Oct 06, 2021)
16-764085-G-A		not specified	Uncertain significance (Nov 10, 2021)
16-764649-G-T			Benign (Jun 10, 2018)
16-764651-G-A		not specified	Uncertain significance (May 15, 2024)
16-764666-G-A		not specified	Uncertain significance (Jun 10, 2024)
16-764911-G-C		not specified	Uncertain significance (Apr 29, 2024)
16-764946-C-G		not specified	Uncertain significance (Mar 19, 2024)
16-764954-G-A		not specified	Uncertain significance (Jun 02, 2024)
16-764960-C-T		not specified	Uncertain significance (Feb 15, 2023)
16-764995-C-T		not specified	Uncertain significance (Dec 26, 2023)
16-764998-G-A		not specified	Uncertain significance (Jun 03, 2022)
16-765147-G-A		not specified	Likely benign (Dec 26, 2023)
16-765195-A-T		not specified	Uncertain significance (Jun 17, 2024)
16-765202-C-T			Benign (Nov 09, 2017)
16-765215-C-A		not specified	Uncertain significance (Sep 16, 2021)
16-765273-C-G		not specified	Uncertain significance (Dec 19, 2023)
16-765287-G-A		not specified	Uncertain significance (Sep 16, 2021)
16-765296-C-T		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MSLN	protein_coding	protein_coding	ENST00000382862	16	8104

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.88e-25	0.0000961	124844	0	133	124977	0.000532

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.04	474	414	1.14	0.0000291	3944
Missense in Polyphen		111	104.96	1.0576		1233
Synonymous	-2.69	242	194	1.25	0.0000138	1400
Loss of Function	-0.590	35	31.4	1.11	0.00000149	338

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00249	0.00248
Ashkenazi Jewish	0.00	0.00
East Asian	0.000711	0.000708
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.000300	0.000293
Middle Eastern	0.000711	0.000708
South Asian	0.000342	0.000294
Other	0.000492	0.000492

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Membrane-anchored forms may play a role in cellular adhesion.
• Disease: DISEASE: Note=Antibodies against MSLN are detected in patients with mesothelioma and ovarian cancer. {ECO:0000269|PubMed:15897581}.
• Pathway: Post-translational protein phosphorylation;Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

• pRec: 0.200

Intolerance Scores

• loftool: 0.920
• rvis_EVS: 0.73
• rvis_percentile_EVS: 85.99

Haploinsufficiency Scores

• pHI: 0.0594
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.282

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Msln
• Phenotype: normal phenotype

Gene ontology

• Biological process: cell adhesion;cell-matrix adhesion;pancreas development;post-translational protein modification;cellular protein metabolic process
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum lumen;Golgi apparatus;plasma membrane;cell surface;membrane;anchored component of membrane
• Molecular function: protein binding