TIGD4

tigger transposable element derived 4, the group of DNA transposon derived genes|Helix-turn-helix CENPB type domain containing

Basic information

Region (hg38): 4:152769354-152779730

Links

ENSG00000169989 ∙ NCBI:201798 ∙ ∙ HGNC:18335 ∙ Uniprot:Q8IY51 ∙ 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 TIGD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TIGD4 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						0
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	0

Variants in TIGD4

This is a list of pathogenic ClinVar variants found in the TIGD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-152769515-T-G		not specified	Uncertain significance (Feb 27, 2024)
4-152769537-C-T		not specified	Uncertain significance (Apr 28, 2023)
4-152769560-A-C		not specified	Uncertain significance (Dec 12, 2024)
4-152769564-T-G		not specified	Uncertain significance (Dec 03, 2021)
4-152769576-T-A		not specified	Uncertain significance (Jan 07, 2022)
4-152769590-T-C		not specified	Uncertain significance (Jan 23, 2024)
4-152769669-A-G		not specified	Uncertain significance (Jul 09, 2024)
4-152769744-C-T		not specified	Uncertain significance (Feb 12, 2025)
4-152769782-C-G		not specified	Uncertain significance (Feb 06, 2023)
4-152769881-T-G		not specified	Uncertain significance (Nov 17, 2022)
4-152769888-T-C		not specified	Uncertain significance (Mar 31, 2022)
4-152769891-C-A		not specified	Uncertain significance (Jan 04, 2024)
4-152769891-C-T		not specified	Uncertain significance (Jul 05, 2023)
4-152769905-G-C		not specified	Uncertain significance (Feb 24, 2025)
4-152769909-C-T		not specified	Uncertain significance (Jun 27, 2023)
4-152770059-T-C		not specified	Likely benign (Apr 06, 2022)
4-152770067-G-T		not specified	Uncertain significance (Jan 17, 2025)
4-152770113-T-G		not specified	Uncertain significance (Jul 07, 2024)
4-152770169-T-C		not specified	Uncertain significance (Sep 12, 2023)
4-152770188-C-T		not specified	Uncertain significance (Dec 22, 2023)
4-152770209-C-T		not specified	Uncertain significance (Apr 19, 2024)
4-152770257-C-T		not specified	Uncertain significance (May 08, 2023)
4-152770293-T-C		not specified	Uncertain significance (May 08, 2023)
4-152770403-C-T		not specified	Uncertain significance (Nov 21, 2023)
4-152770421-T-C		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TIGD4	protein_coding	protein_coding	ENST00000304337	1	10411

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.34e-8	0.414	125005	5	718	125728	0.00288

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.156	254	261	0.973	0.0000122	3348
Missense in Polyphen		78	92.737	0.84109		1199
Synonymous	0.724	87	96.0	0.906	0.00000460	1000
Loss of Function	0.790	13	16.5	0.790	9.68e-7	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00366	0.00365
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000490	0.000489
Finnish	0.00143	0.00143
European (Non-Finnish)	0.00413	0.00411
Middle Eastern	0.000490	0.000489
South Asian	0.00351	0.00344
Other	0.00327	0.00326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.945
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.69

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.310

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.483

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tigd4

Gene ontology

• Cellular component: nucleus
• Molecular function: DNA binding