TASP1

taspase 1

Basic information

Region (hg38): 20:13389392-13638932

Previous symbols: [ "C20orf13" ]

Links

ENSG00000089123 ∙ NCBI:55617 ∙ OMIM:608270 ∙ HGNC:15859 ∙ Uniprot:Q9H6P5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Suleiman-El-Hattab syndrome (Moderate), mode of inheritance: AR
• Suleiman-El-Hattab syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Suleiman-El-Hattab syndrome	AR	Allergy/Immunology/Infectious; Cardiovascular	Among other features, individuals have been described with recurrent respiratory infections, and awareness may allow management of these sequelae; The condition can involve congenital cardiac anomalies, and awareness may allow early management	Allergy/Immunology/Infectious; Cardiovascular; Craniofacial; Musculoskeletal; Neurologic	31209944

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TASP1 gene.

• Global developmental delay (1 variants)
• Suleiman-El-Hattab syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TASP1 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				2	2	4
missense		1	16	2		19
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		2				2
splice region				3	6	9
non coding			1			1
Total	1	3	17	4	2

Variants in TASP1

This is a list of pathogenic ClinVar variants found in the TASP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-13390425-C-T		Inborn genetic diseases	Uncertain significance (Oct 25, 2022)
20-13390451-G-C		Inborn genetic diseases	Uncertain significance (Feb 15, 2023)
20-13390456-CAG-C		TASP1-related disorder	Likely benign (Dec 16, 2019)
20-13417495-C-T		Inborn genetic diseases	Uncertain significance (Dec 06, 2021)
20-13435077-G-T		Inborn genetic diseases	Uncertain significance (Jun 28, 2023)
20-13435080-C-T		Inborn genetic diseases	Uncertain significance (Aug 10, 2021)
20-13435113-C-T			Uncertain significance (Jul 28, 2020)
20-13435116-C-T		Suleiman-El-Hattab syndrome	Uncertain significance (Apr 26, 2024)
20-13483235-T-C		Suleiman-El-Hattab syndrome	Uncertain significance (Jan 31, 2022)
20-13483309-T-C		Inborn genetic diseases	Uncertain significance (Jul 13, 2021)
20-13483347-C-T		Suleiman-El-Hattab syndrome	Uncertain significance (Feb 22, 2022)
20-13534015-T-C		TASP1-related disorder	Benign (Jan 27, 2020)
20-13534052-C-T		TASP1-related disorder	Benign (Nov 12, 2019)
20-13534091-G-A			Likely benign (Aug 01, 2022)
20-13534116-G-A		Abnormal facial shape;Happy demeanor;Global developmental delay • Suleiman-El-Hattab syndrome	Likely pathogenic (Mar 14, 2024)
20-13534126-T-C		Inborn genetic diseases	Uncertain significance (Oct 25, 2022)
20-13559007-C-A		Suleiman-El-Hattab syndrome	Likely pathogenic (Dec 07, 2022)
20-13559038-T-A		TASP1-related disorder	Likely benign (Mar 15, 2022)
20-13559042-A-T		TASP1-related disorder • Inborn genetic diseases	Uncertain significance (Oct 10, 2023)
20-13559094-T-C		Inborn genetic diseases	Uncertain significance (Apr 01, 2024)
20-13569512-G-A		Inborn genetic diseases	Uncertain significance (Aug 12, 2022)
20-13569524-G-A		Inborn genetic diseases	Uncertain significance (May 01, 2024)
20-13569567-C-T		Suleiman-El-Hattab syndrome	Uncertain significance (Jan 18, 2023)
20-13580926-G-A		Suleiman-El-Hattab syndrome	Uncertain significance (Apr 26, 2024)
20-13580983-T-C		Suleiman-El-Hattab syndrome	Likely pathogenic (Jan 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TASP1	protein_coding	protein_coding	ENST00000337743	13	372879

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.608	0.392	125732	0	10	125742	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	159	226	0.704	0.0000114	2689
Missense in Polyphen		25	71.404	0.35012		771
Synonymous	-0.133	88	86.4	1.02	0.00000511	827
Loss of Function	3.68	5	24.8	0.202	0.00000124	317

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000949	0.0000907
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.0000447	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000358	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protease involved in KMT2A/MLL1 processing and, consequently, in the correct expression of the early HOXA gene cluster. {ECO:0000269|PubMed:14636557}.

Recessive Scores

• pRec: 0.241

Intolerance Scores

• loftool: 0.156
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.213
• hipred: Y
• hipred_score: 0.728
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.734

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tasp1
• Phenotype: immune system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; hematopoietic system phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: proteolysis;positive regulation of transcription, DNA-templated;protein maturation
• Cellular component: cytoplasm
• Molecular function: threonine-type endopeptidase activity;hydrolase activity;identical protein binding