MAST3

microtubule associated serine/threonine kinase 3, the group of AGC family kinases|PDZ domain containing

Basic information

Region (hg38): 19:18097778-18151692

Links

ENSG00000099308 ∙ NCBI:23031 ∙ OMIM:612258 ∙ HGNC:19036 ∙ Uniprot:O60307 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• developmental and epileptic encephalopathy 108 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 108	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	34185323; 35095415

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MAST3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAST3 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					3	3
missense		1	67	20	2	90
nonsense			2			2
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			3	2		5
non coding					2	2
Total	0	1	70	20	7

Variants in MAST3

This is a list of pathogenic ClinVar variants found in the MAST3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-18097815-G-A		MAST3-related disorder	Uncertain significance (Nov 08, 2023)
19-18097827-T-C			Uncertain significance (Dec 22, 2023)
19-18098768-A-G		IL12RB1-related disorder	Benign (Jan 11, 2024)
19-18107615-G-A		Inborn genetic diseases	Uncertain significance (Jun 09, 2022)
19-18107624-T-G			Uncertain significance (Mar 04, 2024)
19-18121692-A-G		Inborn genetic diseases	Uncertain significance (Oct 08, 2024)
19-18121701-C-T		Inborn genetic diseases	Uncertain significance (Oct 06, 2022)
19-18121743-C-G			Uncertain significance (May 31, 2022)
19-18121762-C-T		Inborn genetic diseases	Uncertain significance (Sep 25, 2023)
19-18122679-C-A		MAST3-related disorder	Uncertain significance (Sep 20, 2024)
19-18122679-C-T		MAST3-related disorder	Likely benign (Sep 06, 2024)
19-18122679-CG-GA			Uncertain significance (Mar 14, 2022)
19-18122691-G-T		Inborn genetic diseases	Uncertain significance (Dec 01, 2022)
19-18122750-C-T			Pathogenic (Jun 21, 2023)
19-18122754-A-G			Uncertain significance (Jun 12, 2023)
19-18123229-TC-T			Uncertain significance (May 21, 2024)
19-18123296-A-G			Uncertain significance (Apr 16, 2021)
19-18123334-G-A			Likely benign (Mar 01, 2024)
19-18123346-C-T		Inborn genetic diseases	Likely benign (Dec 09, 2023)
19-18123582-C-T		Inborn genetic diseases	Uncertain significance (Jun 28, 2024)
19-18123605-G-A		Inborn genetic diseases	Uncertain significance (Aug 01, 2022)
19-18123610-T-G		Inborn genetic diseases	Uncertain significance (Jan 19, 2024)
19-18123639-G-A		Inborn genetic diseases	Uncertain significance (Nov 27, 2024)
19-18123961-G-A		Inborn genetic diseases	Likely benign (Dec 18, 2023)
19-18123979-C-T			Benign (Dec 20, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAST3	protein_coding	protein_coding	ENST00000262811	27	53900

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000937	125513	0	13	125526	0.0000518

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.14	510	849	0.601	0.0000614	8281
Missense in Polyphen		136	327.66	0.41506		3149
Synonymous	0.857	346	367	0.943	0.0000269	2799
Loss of Function	5.97	6	52.8	0.114	0.00000275	608

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000187	0.000183
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000560	0.0000544
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.0000624	0.0000528
Middle Eastern	0.0000560	0.0000544
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.285
• rvis_EVS: -1.55
• rvis_percentile_EVS: 3.31

Haploinsufficiency Scores

• pHI: 0.305
• hipred: Y
• hipred_score: 0.681
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.818

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mast3

Gene ontology

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