MST1

macrophage stimulating 1

Basic information

Region (hg38): 3:49683947-49689501

Previous symbols: [ "D3F15S2", "HGFL", "DNF15S2" ]

Links

ENSG00000173531 ∙ NCBI:4485 ∙ OMIM:142408 ∙ HGNC:7380 ∙ Uniprot:P26927 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• epidermodysplasia verruciformis (Moderate), mode of inheritance: Unknown
• combined immunodeficiency due to STK4 deficiency (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MST1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MST1 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				6		6
missense			70	6	1	77
nonsense					1	1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	71	12	2

Variants in MST1

This is a list of pathogenic ClinVar variants found in the MST1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-49684033-C-T		not specified	Uncertain significance (Dec 21, 2021)
3-49684080-G-A		not specified	Likely benign (Oct 07, 2024)
3-49684098-C-T		not specified	Uncertain significance (Dec 06, 2024)
3-49684102-A-G		not specified	Likely benign (Sep 03, 2024)
3-49684108-C-T		not specified	Uncertain significance (Sep 30, 2024)
3-49684116-C-T		not specified	Uncertain significance (Dec 21, 2022)
3-49684119-T-C		not specified	Uncertain significance (Aug 06, 2024)
3-49684144-C-T		not specified	Uncertain significance (May 26, 2023)
3-49684159-T-C		not specified	Uncertain significance (Jul 09, 2021)
3-49684189-C-T		not specified	Uncertain significance (Aug 02, 2021)
3-49684327-A-C		not specified	Uncertain significance (May 12, 2024)
3-49684364-C-G		not specified	Uncertain significance (Dec 14, 2023)
3-49684373-G-T		not specified	Uncertain significance (Dec 21, 2022)
3-49684378-C-T		not specified	Uncertain significance (Aug 23, 2021)
3-49684379-G-A			Benign (Jan 01, 2025)
3-49684393-C-T		not specified	Uncertain significance (Jun 06, 2023)
3-49684430-T-G		not specified	Uncertain significance (Apr 22, 2022)
3-49684438-G-A		not specified	Uncertain significance (Nov 07, 2024)
3-49684598-C-T		not specified	Uncertain significance (Jun 07, 2024)
3-49684636-C-T		not specified	Uncertain significance (Nov 13, 2024)
3-49684742-C-T		not specified	Uncertain significance (Dec 13, 2021)
3-49684753-A-G		not specified	Uncertain significance (Jul 19, 2023)
3-49684859-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-49685030-C-T		not specified	Uncertain significance (Mar 30, 2024)
3-49685031-G-A		not specified	Uncertain significance (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MST1	protein_coding	protein_coding	ENST00000449682	18	5555

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.78e-19	0.143	122424	21	3170	125615	0.0128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.531	482	450	1.07	0.0000282	4639
Missense in Polyphen		178	153.75	1.1577		1674
Synonymous	-1.05	191	173	1.10	0.0000102	1408
Loss of Function	1.38	34	43.9	0.775	0.00000212	447

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0121	0.0119
Ashkenazi Jewish	0.0218	0.0219
East Asian	0.000934	0.000925
Finnish	0.00573	0.00574
European (Non-Finnish)	0.0168	0.0168
Middle Eastern	0.000934	0.000925
South Asian	0.0174	0.0173
Other	0.0147	0.0148

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=MST1 variant Cys-689 may be associated with inflammatory bowel disease (IBD), a chronic, relapsing inflammation of the gastrointestinal tract with a complex etiology. It is unsure whether Cys-689 itself or a variation in linkage disequilibrium with Cys-689 is responsible for the association with IBD. {ECO:0000269|PubMed:19079170, ECO:0000269|PubMed:20228799}.
• Pathway: Signal Transduction;a6b1 and a6b4 Integrin signaling;Signaling by MST1;Signaling by Receptor Tyrosine Kinases;amb2 Integrin signaling;FoxO family signaling (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.148
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.79

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.351
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.421

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mst1
• Phenotype: immune system phenotype; liver/biliary system phenotype; hematopoietic system phenotype; digestive/alimentary phenotype

Zebrafish Information Network

• Gene name: mst1
• Affected structure: intestinal epithelial cell
• Phenotype tag: abnormal
• Phenotype quality: increased rate

Gene ontology

• Biological process: proteolysis;regulation of macrophage chemotaxis;positive regulation of mammary gland epithelial cell proliferation;negative regulation of gluconeogenesis;hepatocyte growth factor receptor signaling pathway;regulation of cAMP-dependent protein kinase activity
• Cellular component: extracellular region;extracellular space
• Molecular function: serine-type endopeptidase activity;protein binding;receptor tyrosine kinase binding