TLL2

tolloid like 2, the group of Astacins

Basic information

Region (hg38): 10:96364608-96513926

Links

ENSG00000095587 ∙ NCBI:7093 ∙ OMIM:606743 ∙ HGNC:11844 ∙ Uniprot:Q9Y6L7 ∙ 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 TLL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLL2 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
missense			66	3	4	73
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	66	3	6

Variants in TLL2

This is a list of pathogenic ClinVar variants found in the TLL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-96368135-G-C		not specified	Uncertain significance (Sep 29, 2023)
10-96368173-C-T		not specified	Likely benign (Nov 09, 2021)
10-96368174-G-A		not specified	Uncertain significance (Jul 14, 2021)
10-96368203-G-A		not specified	Uncertain significance (Aug 01, 2022)
10-96368216-C-T		not specified	Uncertain significance (May 09, 2023)
10-96370072-C-T		not specified	Uncertain significance (Apr 15, 2024)
10-96370085-C-A		not specified	Uncertain significance (Jun 30, 2023)
10-96370238-G-A		not specified	Uncertain significance (Jun 27, 2022)
10-96370242-G-A			Benign (Jan 31, 2018)
10-96370255-A-G		not specified	Uncertain significance (Oct 14, 2023)
10-96370258-T-C		not specified	Uncertain significance (Dec 28, 2023)
10-96370310-C-A		not specified	Uncertain significance (Dec 04, 2023)
10-96373613-T-C		not specified	Uncertain significance (Nov 10, 2022)
10-96373628-T-C		not specified	Uncertain significance (Jan 22, 2024)
10-96373671-C-T		not specified	Uncertain significance (Mar 22, 2023)
10-96373682-G-A		not specified	Likely benign (Sep 29, 2023)
10-96373704-C-T		not specified	Uncertain significance (Sep 17, 2021)
10-96373733-C-T		not specified	Uncertain significance (Sep 15, 2021)
10-96373739-G-A		not specified	Uncertain significance (Oct 03, 2022)
10-96373746-C-T		not specified	Uncertain significance (Dec 16, 2023)
10-96373780-G-C		not specified	Uncertain significance (Apr 23, 2024)
10-96376744-C-T		not specified	Uncertain significance (Apr 09, 2024)
10-96376778-C-T		not specified	Uncertain significance (Dec 07, 2023)
10-96376780-A-C		not specified	Uncertain significance (Oct 03, 2023)
10-96379006-C-T		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLL2	protein_coding	protein_coding	ENST00000357947	21	149313

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.14e-31	0.000289	125520	0	228	125748	0.000907

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.447	596	628	0.950	0.0000379	6706
Missense in Polyphen		200	204.55	0.97777		2130
Synonymous	1.61	224	257	0.872	0.0000177	1886
Loss of Function	0.623	50	55.0	0.909	0.00000284	611

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00194	0.00193
Ashkenazi Jewish	0.000115	0.0000992
East Asian	0.00142	0.00141
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000946	0.000915
Middle Eastern	0.00142	0.00141
South Asian	0.00160	0.00154
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protease which specifically processes pro-lysyl oxidase. Required for the embryonic development. Predominant protease, which in the development, influences dorsal-ventral patterning and skeletogenesis.
• Pathway: Crosslinking of collagen fibrils;Assembly of collagen fibrils and other multimeric structures;Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization;DroToll-like;Anchoring fibril formation;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.760
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.74

Haploinsufficiency Scores

• pHI: 0.228
• hipred: N
• hipred_score: 0.251
• ghis: 0.452

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.204

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tll2
• Phenotype: muscle phenotype

Gene ontology

• Biological process: proteolysis;multicellular organism development;extracellular matrix disassembly;cell differentiation;negative regulation of skeletal muscle tissue growth
• Cellular component: extracellular region
• Molecular function: metalloendopeptidase activity;serine-type endopeptidase activity;calcium ion binding;zinc ion binding