TGM4

transglutaminase 4, the group of Transglutaminases

Basic information

Region (hg38): 3:44874608-44914990

Links

ENSG00000163810 ∙ NCBI:7047 ∙ OMIM:600585 ∙ HGNC:11780 ∙ Uniprot:P49221 ∙ 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 TGM4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TGM4 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				1	3	4
missense			38	1	1	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	2	4

Variants in TGM4

This is a list of pathogenic ClinVar variants found in the TGM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-44885343-T-C		not specified	Uncertain significance (May 31, 2023)
3-44885368-C-T			Benign (Apr 20, 2018)
3-44885382-C-T		not specified	Uncertain significance (Jan 17, 2023)
3-44885414-C-A			Benign (May 18, 2018)
3-44885418-G-A		not specified	Uncertain significance (Sep 20, 2023)
3-44885438-C-T		not specified	Uncertain significance (Apr 09, 2024)
3-44887789-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
3-44893586-T-C		not specified	Uncertain significance (Jan 17, 2024)
3-44893601-A-T		not specified	Uncertain significance (Feb 06, 2024)
3-44893634-C-T		not specified	Uncertain significance (Jan 08, 2024)
3-44893673-G-A		not specified	Likely benign (Jun 06, 2022)
3-44896773-A-T		not specified	Uncertain significance (Nov 03, 2023)
3-44896776-G-A		not specified	Uncertain significance (Apr 05, 2023)
3-44896807-G-A		not specified	Uncertain significance (Oct 22, 2021)
3-44901576-A-G		not specified	Uncertain significance (Feb 28, 2024)
3-44901599-A-G		not specified	Uncertain significance (Jan 10, 2022)
3-44901642-C-T		not specified	Uncertain significance (May 05, 2023)
3-44901671-T-C		not specified	Uncertain significance (Oct 27, 2022)
3-44901672-G-A		Essential tremor	Likely pathogenic (-)
3-44901823-G-A		not specified	Uncertain significance (Apr 14, 2022)
3-44901858-A-G		not specified	Uncertain significance (Jul 26, 2021)
3-44901888-G-A		not specified	Uncertain significance (May 29, 2024)
3-44901909-A-C		not specified	Uncertain significance (Feb 05, 2024)
3-44903904-A-C		not specified	Uncertain significance (Feb 01, 2023)
3-44903930-C-T		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TGM4	protein_coding	protein_coding	ENST00000296125	14	40383

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.80e-20	0.00916	123212	24	2511	125747	0.0101

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0135	386	387	0.998	0.0000212	4508
Missense in Polyphen		134	125.1	1.0711		1427
Synonymous	-0.781	176	163	1.08	0.0000105	1302
Loss of Function	0.564	32	35.6	0.898	0.00000188	379

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0102	0.0102
Ashkenazi Jewish	0.0226	0.0226
East Asian	0.000979	0.000979
Finnish	0.0118	0.0116
European (Non-Finnish)	0.00995	0.00990
Middle Eastern	0.000979	0.000979
South Asian	0.0174	0.0173
Other	0.0122	0.0121

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associated with the mammalian reproductive process. Catalyzes the cross-linking of proteins and the conjugation of polyamines to specific proteins in the seminal tract.

Recessive Scores

• pRec: 0.472

Intolerance Scores

• loftool: 0.284
• rvis_EVS: 0.9
• rvis_percentile_EVS: 89.31

Haploinsufficiency Scores

• pHI: 0.0609
• 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: 0.00602

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tgm4
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: peptide cross-linking
• Cellular component: cytoplasm;Golgi apparatus;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: protein-glutamine gamma-glutamyltransferase activity;metal ion binding