TIGD2

tigger transposable element derived 2, the group of DNA transposon derived genes|Helix-turn-helix CENPB type domain containing

Basic information

Region (hg38): 4:89111533-89114901

Links

ENSG00000180346 ∙ NCBI:166815 ∙ OMIM:612973 ∙ HGNC:18333 ∙ Uniprot:Q4W5G0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TIGD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TIGD2 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in TIGD2

This is a list of pathogenic ClinVar variants found in the TIGD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-89113044-G-A		not specified	Uncertain significance (Mar 17, 2023)
4-89113081-G-C		not specified	Uncertain significance (Aug 14, 2023)
4-89113110-A-G		not specified	Uncertain significance (Jun 21, 2022)
4-89113242-C-A		not specified	Uncertain significance (Jun 05, 2024)
4-89113308-G-A		not specified	Uncertain significance (Apr 26, 2023)
4-89113320-G-A		not specified	Uncertain significance (Feb 07, 2023)
4-89113333-A-G		not specified	Uncertain significance (Dec 20, 2023)
4-89113444-G-A		not specified	Uncertain significance (Nov 18, 2022)
4-89113525-A-G		not specified	Uncertain significance (Oct 05, 2023)
4-89113556-A-C		not specified	Uncertain significance (May 13, 2024)
4-89113572-T-C		not specified	Uncertain significance (Dec 07, 2023)
4-89113573-C-T		not specified	Uncertain significance (May 16, 2023)
4-89113617-G-A		not specified	Uncertain significance (May 05, 2023)
4-89113758-T-C		not specified	Uncertain significance (Mar 30, 2024)
4-89114151-G-C		not specified	Uncertain significance (Apr 06, 2024)
4-89114173-T-C		not specified	Uncertain significance (Sep 13, 2022)
4-89114197-C-A		not specified	Uncertain significance (Sep 17, 2021)
4-89114239-A-C		not specified	Uncertain significance (May 14, 2024)
4-89114239-A-G		not specified	Uncertain significance (Sep 26, 2023)
4-89114247-A-G		not specified	Uncertain significance (Jun 16, 2023)
4-89114248-T-C		not specified	Uncertain significance (Feb 13, 2024)
4-89114349-C-A		not specified	Uncertain significance (Oct 12, 2022)
4-89114400-A-G		not specified	Uncertain significance (Nov 09, 2022)
4-89114413-C-T		not specified	Uncertain significance (Jun 02, 2023)
4-89114427-A-G		not specified	Uncertain significance (Sep 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TIGD2	protein_coding	protein_coding	ENST00000317005	1	2083

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000529	0.972	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.486	256	279	0.918	0.0000143	3470
Missense in Polyphen		62	108.15	0.57328		1324
Synonymous	0.618	88	95.7	0.920	0.00000483	976
Loss of Function	1.98	10	19.4	0.516	0.00000104	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.689
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.242
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.296

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tigd2

Gene ontology

• Cellular component: nucleus
• Molecular function: DNA binding