TIGD6

tigger transposable element derived 6, the group of Helix-turn-helix CENPB type domain containing|DNA transposon derived genes

Basic information

Region (hg38): 5:149993118-150000654

Links

ENSG00000164296 ∙ NCBI:81789 ∙ ∙ HGNC:18332 ∙ Uniprot:Q17RP2 ∙ 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 TIGD6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TIGD6 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			51	1		52
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	51	1	1

Variants in TIGD6

This is a list of pathogenic ClinVar variants found in the TIGD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-149994833-T-G		not specified	Uncertain significance (Jan 27, 2025)
5-149994836-C-T		not specified	Uncertain significance (Jan 27, 2025)
5-149994876-A-C		not specified	Uncertain significance (Jun 03, 2024)
5-149994901-C-G		not specified	Uncertain significance (Jun 07, 2024)
5-149994937-G-A		not specified	Uncertain significance (Mar 19, 2024)
5-149994941-T-C		not specified	Uncertain significance (Jan 23, 2025)
5-149994990-T-A		not specified	Uncertain significance (Aug 20, 2024)
5-149995055-C-T		not specified	Uncertain significance (Dec 16, 2024)
5-149995064-T-G		not specified	Uncertain significance (Apr 07, 2023)
5-149995100-A-G		not specified	Uncertain significance (Dec 06, 2022)
5-149995130-T-C		not specified	Uncertain significance (Apr 22, 2022)
5-149995132-G-T		not specified	Uncertain significance (Jan 16, 2024)
5-149995157-T-C		not specified	Uncertain significance (Feb 19, 2025)
5-149995210-A-G		not specified	Uncertain significance (Oct 26, 2021)
5-149995267-C-A		not specified	Uncertain significance (Feb 28, 2023)
5-149995273-G-A		not specified	Uncertain significance (Apr 16, 2024)
5-149995286-T-C		not specified	Uncertain significance (Mar 05, 2025)
5-149995312-T-A		not specified	Uncertain significance (Mar 23, 2022)
5-149995316-CT-C			Benign (Oct 17, 2019)
5-149995340-T-C		not specified	Uncertain significance (Jul 27, 2024)
5-149995395-T-C		not specified	Uncertain significance (Jan 27, 2022)
5-149995431-G-C		not specified	Uncertain significance (Jul 20, 2021)
5-149995438-G-C		not specified	Uncertain significance (Feb 28, 2024)
5-149995517-G-A		not specified	Uncertain significance (Feb 14, 2025)
5-149995519-C-T		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TIGD6	protein_coding	protein_coding	ENST00000296736	1	8050

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000480	0.657	19525	46736	59487	125748	0.606

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.317	291	276	1.05	0.0000144	3477
Missense in Polyphen		49	59.511	0.82338		803
Synonymous	-0.252	103	99.8	1.03	0.00000520	998
Loss of Function	0.995	10	14.0	0.713	6.93e-7	178

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	1.15	1.11
Ashkenazi Jewish	0.615	0.620
East Asian	0.624	0.619
Finnish	0.675	0.675
European (Non-Finnish)	0.657	0.652
Middle Eastern	0.624	0.619
South Asian	0.588	0.584
Other	0.622	0.612

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.938
• rvis_EVS: 1.36
• rvis_percentile_EVS: 94.41

Haploinsufficiency Scores

• pHI: 0.105
• 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: 0.00141

Gene Damage Prediction

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

Gene ontology

• Cellular component: nucleus
• Molecular function: DNA binding