TIGD1

tigger transposable element derived 1, the group of DNA transposon derived genes|Helix-turn-helix CENPB type domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 2:232543883-232550557

Links

ENSG00000221944 ∙ NCBI:200765 ∙ OMIM:612972 ∙ HGNC:14523 ∙ Uniprot:Q96MW7 ∙ 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 TIGD1 gene.

• not provided (6 variants)
• Lethal multiple pterygium syndrome (1 variants)
• Autosomal recessive multiple pterygium syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TIGD1 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				1		1
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	7	3	43	71	9	133
Total	7	3	43	72	9

Highest pathogenic variant AF is 0.00000657

Variants in TIGD1

This is a list of pathogenic ClinVar variants found in the TIGD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-232544303-G-A			Benign (Nov 12, 2018)
2-232544357-C-T			Likely benign (Jan 17, 2023)
2-232544358-C-T			Likely benign (Nov 10, 2023)
2-232544358-CCT-C		Autosomal recessive multiple pterygium syndrome	Conflicting classifications of pathogenicity (Jan 22, 2024)
2-232544359-C-T			Likely benign (Jan 11, 2024)
2-232544359-CT-C			Likely benign (Mar 10, 2023)
2-232544372-C-T			Likely benign (Mar 18, 2023)
2-232544384-G-A			Likely benign (Sep 30, 2023)
2-232544387-C-T			Likely benign (Nov 21, 2023)
2-232544390-G-A			Likely benign (Jan 18, 2024)
2-232544393-G-C			Likely benign (Jan 15, 2024)
2-232544405-C-T		Autosomal recessive multiple pterygium syndrome • Lethal multiple pterygium syndrome	Conflicting classifications of pathogenicity (Jan 26, 2024)
2-232544406-G-A		Autosomal recessive multiple pterygium syndrome • Lethal multiple pterygium syndrome • Inborn genetic diseases	Uncertain significance (Jun 03, 2024)
2-232544407-T-G		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
2-232544409-CGCCCGCTGGCCCCGGCAGCTGT-C			Pathogenic (Aug 29, 2023)
2-232544410-G-A		Inborn genetic diseases	Uncertain significance (Apr 12, 2022)
2-232544414-G-A			Likely benign (Aug 10, 2023)
2-232544422-C-T			Uncertain significance (Jul 21, 2016)
2-232544423-G-A			Likely benign (Jan 08, 2024)
2-232544425-C-G		Inborn genetic diseases	Uncertain significance (Apr 27, 2024)
2-232544431-T-C			Conflicting classifications of pathogenicity (Jan 30, 2024)
2-232544436-G-A		Lethal multiple pterygium syndrome • Autosomal recessive multiple pterygium syndrome	Uncertain significance (Jan 12, 2018)
2-232544446-C-T		Autosomal recessive multiple pterygium syndrome;Lethal multiple pterygium syndrome • Lethal multiple pterygium syndrome • Autosomal recessive multiple pterygium syndrome • CHRNG-related disorder	Conflicting classifications of pathogenicity (Jan 29, 2024)
2-232544449-G-A		Lethal multiple pterygium syndrome • Autosomal recessive multiple pterygium syndrome	Uncertain significance (Mar 07, 2022)
2-232544454-C-T			Pathogenic (Dec 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TIGD1	protein_coding	protein_coding	ENST00000408957	1	2448

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00368	0.857	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.404	234	217	1.08	0.0000108	3856
Missense in Polyphen		54	50.565	1.0679		930
Synonymous	0.327	73	76.6	0.952	0.00000376	1103
Loss of Function	1.24	5	9.02	0.554	5.49e-7	156

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

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.308

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