TIGD4

protein-coding

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

Gene summary

The protein encoded by this gene belongs to the tigger subfamily of the pogo superfamily of DNA-mediated transposons in humans. These proteins are related to DNA transposons found in fungi and nematodes, and more distantly to the Tc1 and mariner transposases. They are also very similar to the major mammalian centromere protein B. The exact function of this gene is not known. [provided by RefSeq, Jul 2008]

MANE transcript

NM_145720.4

Inheritance

—

ClinVar variants

U:54B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr4:152,769,354-152,779,730

External References & Databases

Ensembl (ENSG00000169989)

Transcript & Mutation Effects

hg38 • Region Span ~10.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TIGD4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 55

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145720.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			54 clinvar	1 clinvar		55
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	54	1	0	55

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145720.4	RefSeq	NP_663772.1	1	MANE Select
ENST00000304337.3	Ensembl	ENSP00000355162.2	1	MANE Select
ENST00000891947.1	Ensembl	ENSP00000562006.1	1	Standard
ENST00000891947.2	Ensembl	ENSP00000562006.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

DNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000304337
Coding exons: 1
Length: 10411
Individuals with no LoFs: 125005
Homozygous LoFs: 5
Heterozygous LoFs: 718
Defined: 125728
p: 0.00288

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.156	254	261	0.973	0.0000122	3348
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0020	0.0020	notable
Latino/Admixed American	0.0016	0.0016	notable
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00049	0.00049	rare
Finnish	0.0014	0.0014	notable
European (Non-Finnish)	0.0041	0.0041	notable
South Asian	0.0035	0.0034	notable
Other	0.0033	0.0033	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.945
RVIS EVS: 0.46
RVIS percentile EVS: 78.69

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.483

Gene Damage Prediction

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