TGM7

transglutaminase 7, the group of Transglutaminases

Basic information

Region (hg38): 15:43276271-43302255

Links

ENSG00000159495 ∙ NCBI:116179 ∙ OMIM:606776 ∙ HGNC:30790 ∙ Uniprot:Q96PF1 ∙ 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 TGM7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TGM7 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			47	2		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	5	0

Variants in TGM7

This is a list of pathogenic ClinVar variants found in the TGM7 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-43276477-A-T		not specified	Uncertain significance (Jan 10, 2023)
15-43276514-C-T		not specified	Uncertain significance (Feb 16, 2023)
15-43276526-T-C		not specified	Uncertain significance (Jul 09, 2021)
15-43276870-T-A			Likely benign (Jan 01, 2023)
15-43276880-T-C		not specified	Uncertain significance (Sep 26, 2022)
15-43276967-G-A		not specified	Uncertain significance (Jun 10, 2024)
15-43279130-T-A		not specified	Uncertain significance (Jan 19, 2022)
15-43279148-A-T		not specified	Uncertain significance (Jun 10, 2024)
15-43279167-T-A		not specified	Uncertain significance (Dec 21, 2022)
15-43279182-C-T		not specified	Uncertain significance (Apr 22, 2022)
15-43279187-A-G		not specified	Uncertain significance (Nov 10, 2022)
15-43279204-C-T			Likely benign (Apr 01, 2022)
15-43279209-G-A		not specified	Uncertain significance (Feb 05, 2024)
15-43279229-A-C		not specified	Uncertain significance (Apr 04, 2024)
15-43279254-G-A		not specified	Uncertain significance (May 30, 2024)
15-43279648-C-T		not specified	Uncertain significance (May 24, 2023)
15-43279669-G-A		not specified	Uncertain significance (Jul 25, 2023)
15-43279678-G-A		not specified	Uncertain significance (Jun 11, 2021)
15-43279730-T-C		not specified	Uncertain significance (Oct 25, 2022)
15-43279739-G-A		not specified	Uncertain significance (Mar 07, 2024)
15-43279772-G-A		not specified	Uncertain significance (Jun 27, 2022)
15-43279852-C-T		not specified	Likely benign (Oct 30, 2023)
15-43279856-C-G		not specified	Uncertain significance (Dec 14, 2022)
15-43279931-C-T		not specified	Uncertain significance (May 17, 2023)
15-43281908-G-A			Likely benign (Mar 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TGM7	protein_coding	protein_coding	ENST00000452443	13	25976

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.84e-20	0.0140	125576	0	172	125748	0.000684

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0286	423	425	0.996	0.0000243	4636
Missense in Polyphen		140	145.96	0.95917		1663
Synonymous	0.346	174	180	0.967	0.0000114	1415
Loss of Function	0.681	32	36.4	0.878	0.00000188	367

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00130	0.00128
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.00120	0.00114
Finnish	0.000706	0.000647
European (Non-Finnish)	0.000632	0.000624
Middle Eastern	0.00120	0.00114
South Asian	0.000818	0.000817
Other	0.000816	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the cross-linking of proteins and the conjugation of polyamines to proteins.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.415
• rvis_EVS: 0.12
• rvis_percentile_EVS: 62.17

Haploinsufficiency Scores

• pHI: 0.0772
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tgm7

Gene ontology

• Biological process: peptide cross-linking
• Molecular function: protein-glutamine gamma-glutamyltransferase activity;metal ion binding