TIGD3

tigger transposable element derived 3, the group of Helix-turn-helix CENPB type domain containing|DNA transposon derived genes

Basic information

Region (hg38): 11:65354751-65357613

Links

ENSG00000173825 ∙ NCBI:220359 ∙ OMIM:619084 ∙ HGNC:18334 ∙ Uniprot:Q6B0B8 ∙ 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 TIGD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TIGD3 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in TIGD3

This is a list of pathogenic ClinVar variants found in the TIGD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65355945-C-T		not specified	Uncertain significance (Feb 27, 2024)
11-65355992-G-A		not specified	Uncertain significance (Jun 18, 2021)
11-65356003-C-G		not specified	Uncertain significance (May 23, 2024)
11-65356109-A-G		not specified	Uncertain significance (Oct 02, 2023)
11-65356119-A-G		not specified	Uncertain significance (May 20, 2024)
11-65356122-A-G		not specified	Uncertain significance (Apr 22, 2022)
11-65356136-G-A		not specified	Uncertain significance (Dec 15, 2023)
11-65356205-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-65356209-G-A		not specified	Uncertain significance (Mar 19, 2024)
11-65356248-C-T		not specified	Uncertain significance (Dec 28, 2023)
11-65356278-A-G		not specified	Uncertain significance (Jan 18, 2023)
11-65356344-C-T		not specified	Uncertain significance (Apr 22, 2024)
11-65356373-T-A		not specified	Uncertain significance (Dec 06, 2022)
11-65356485-T-C		not specified	Uncertain significance (Feb 02, 2022)
11-65356505-G-A		not specified	Uncertain significance (May 24, 2023)
11-65356665-C-T		not specified	Uncertain significance (Feb 21, 2024)
11-65356802-G-A		not specified	Likely benign (Jun 04, 2024)
11-65356817-G-A		not specified	Uncertain significance (Oct 02, 2023)
11-65356847-G-A		not specified	Uncertain significance (Apr 11, 2023)
11-65356926-C-T		not specified	Uncertain significance (Dec 21, 2023)
11-65356929-C-G		not specified	Uncertain significance (May 02, 2024)
11-65356964-G-A		not specified	Uncertain significance (Sep 22, 2023)
11-65357042-A-G		not specified	Uncertain significance (Oct 02, 2023)
11-65357079-C-A		not specified	Uncertain significance (Apr 13, 2023)
11-65357079-C-G		not specified	Likely benign (Feb 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TIGD3	protein_coding	protein_coding	ENST00000309880	1	2847

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.63e-10	0.0806	125677	0	68	125745	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.822	254	294	0.865	0.0000196	3009
Missense in Polyphen		55	86.665	0.63463		858
Synonymous	2.85	93	135	0.688	0.00000938	1031
Loss of Function	0.104	15	15.4	0.971	0.00000107	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000326	0.000326
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000309	0.000308
Middle Eastern	0.0000547	0.0000544
South Asian	0.000686	0.000686
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.808
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.56

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.208
• ghis: 0.485

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.118

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tigd3

Gene ontology

• Cellular component: nucleus
• Molecular function: DNA binding