TGIF2LX

TGFB induced factor homeobox 2 like X-linked, the group of TALE class homeoboxes and pseudogenes

Basic information

Region (hg38): X:89921908-89922883

Links

ENSG00000153779 ∙ NCBI:90316 ∙ OMIM:300411 ∙ HGNC:18570 ∙ Uniprot:Q8IUE1 ∙ 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 TGIF2LX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TGIF2LX 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	1

Variants in TGIF2LX

This is a list of pathogenic ClinVar variants found in the TGIF2LX region.

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

Position	Type	Phenotype	Significance	ClinVar
X-89922108-C-T		not specified	Uncertain significance (Dec 09, 2023)
X-89922127-G-A			Benign (Dec 20, 2018)
X-89922139-C-G		not specified	Uncertain significance (Dec 05, 2022)
X-89922177-C-T		not specified	Uncertain significance (Oct 03, 2023)
X-89922192-A-G		not specified	Uncertain significance (Feb 28, 2024)
X-89922431-C-G		not specified	Uncertain significance (Aug 15, 2023)
X-89922506-T-A		not specified	Uncertain significance (Aug 28, 2023)
X-89922621-C-T		not specified	Uncertain significance (Dec 13, 2023)
X-89922683-C-T		not specified	Uncertain significance (Jan 04, 2024)
X-89922686-T-A		not specified	Uncertain significance (Aug 21, 2023)
X-89922737-C-A		not specified	Uncertain significance (Dec 11, 2023)
X-89922749-G-A		not specified	Uncertain significance (Jul 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TGIF2LX	protein_coding	protein_coding	ENST00000561129	1	1002

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.877	82	108	0.762	0.00000929	1569
Missense in Polyphen		18	38.231	0.47082		516
Synonymous	-0.249	55	52.7	1.04	0.00000527	484
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a transcription role in testis.

Recessive Scores

• pRec: 0.0602

Intolerance Scores

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.56

Haploinsufficiency Scores

• pHI: 0.0343
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00373

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tgif2lx2

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding