MAST1

microtubule associated serine/threonine kinase 1, the group of PDZ domain containing|AGC family kinases|MicroRNA protein coding host genes

Basic information

Region (hg38): 19:12833951-12874952

Links

ENSG00000105613 ∙ NCBI:22983 ∙ OMIM:612256 ∙ HGNC:19034 ∙ Uniprot:Q9Y2H9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mega-corpus-callosum syndrome with cerebellar hypoplasia and cortical malformations (Moderate), mode of inheritance: AD
• mega-corpus-callosum syndrome with cerebellar hypoplasia and cortical malformations (Strong), mode of inheritance: AD
• mega-corpus-callosum syndrome with cerebellar hypoplasia and cortical malformations (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mega-corpus-callosum syndrome with cerebellar hypoplasia and cortical malformations	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	30449657

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MAST1 gene.

• Mega-corpus-callosum syndrome with cerebellar hypoplasia and cortical malformations (3 variants)
• not provided (2 variants)
• MAST1-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAST1 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				106	15	121
missense	3	5	186	15	7	216
nonsense	1		4			5
start loss						0
frameshift			3	1		4
inframe indel			5			5
splice donor/acceptor (+/-2bp)			1			1
splice region			7	22	8	37
non coding			3	41	11	55
Total	4	5	202	163	33

Variants in MAST1

This is a list of pathogenic ClinVar variants found in the MAST1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12834789-A-G		not specified	Uncertain significance (Dec 06, 2022)
19-12834832-T-C		not specified	Uncertain significance (Jun 13, 2023)
19-12838566-C-A		MAST1-related disorder	Benign (Dec 09, 2019)
19-12838583-C-T			Uncertain significance (Jul 20, 2023)
19-12838587-C-G			Likely benign (Dec 30, 2023)
19-12838590-G-A			Uncertain significance (Nov 20, 2022)
19-12838660-A-AC			Benign (Nov 06, 2023)
19-12838667-A-T			Likely benign (Dec 03, 2022)
19-12840426-CT-C			Likely benign (Sep 27, 2023)
19-12840438-C-T			Likely benign (May 01, 2023)
19-12840442-G-A			Likely benign (Jul 17, 2022)
19-12840458-T-C			Likely benign (Jun 03, 2023)
19-12840459-A-C			Uncertain significance (Jul 29, 2022)
19-12840463-G-C			Uncertain significance (Jun 07, 2024)
19-12840474-A-G		Inborn genetic diseases	Uncertain significance (Oct 10, 2023)
19-12840503-G-A			Benign (Jul 03, 2023)
19-12840512-C-A		Inborn genetic diseases	Uncertain significance (Jun 02, 2021)
19-12840542-C-T			Likely benign (Apr 30, 2022)
19-12840547-G-A			Likely benign (Sep 01, 2022)
19-12840971-GC-G			Benign (Jul 25, 2022)
19-12840982-C-G			Likely benign (Dec 18, 2023)
19-12840991-GCAGCAGTCCCCTGGA-G			Uncertain significance (Dec 08, 2022)
19-12840993-A-G			Uncertain significance (Jul 23, 2022)
19-12841023-T-TC		Mega-corpus-callosum syndrome with cerebellar hypoplasia and cortical malformations	Uncertain significance (Apr 04, 2022)
19-12841025-C-A			Likely benign (Mar 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAST1	protein_coding	protein_coding	ENST00000251472	26	41001

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.16e-7	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	5.77	514	1.04e+3	0.496	0.0000705	9968
Missense in Polyphen		148	458.01	0.32314		4279
Synonymous	3.03	383	466	0.822	0.0000341	3345
Loss of Function	6.98	5	66.3	0.0754	0.00000349	729

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000945	0.0000924
European (Non-Finnish)	0.0000904	0.0000879
Middle Eastern	0.000164	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Appears to link the dystrophin/utrophin network with microtubule filaments via the syntrophins. Phosphorylation of DMD or UTRN may modulate their affinities for associated proteins (By similarity). {ECO:0000250|UniProtKB:Q9R1L5}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.120
• rvis_EVS: -1.91
• rvis_percentile_EVS: 1.94

Haploinsufficiency Scores

• pHI: 0.493
• hipred: Y
• hipred_score: 0.789
• ghis: 0.654

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mast1

Gene ontology

• Biological process: protein phosphorylation;cytoskeleton organization;peptidyl-serine phosphorylation;intracellular signal transduction
• Cellular component: cytoplasm;cytoskeleton;plasma membrane
• Molecular function: magnesium ion binding;protein serine/threonine kinase activity;protein binding;ATP binding