TGIF2LX

protein-coding

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

Gene summary

This gene encodes a member of the TALE/TGIF homeobox family of transcription factors. Testis-specific expression suggests that this gene may play a role in spermatogenesis. A homolog of this gene lies within the male specific region of chromosome Y, in a block of sequence that is thought to be the result of a large X-to-Y transposition. [provided by RefSeq, Jul 2008]

MANE transcript

NM_138960.4

Inheritance

—

ClinVar variants

U:25B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chrX:89,921,908-89,922,883

External References & Databases

Ensembl (ENSG00000153779)

Transcript & Mutation Effects

hg38 • Region Span ~1.0 kb

Loading mutation effect viewer...

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 TGIF2LX variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 26

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138960.4. 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					1 clinvar	1
missense			25 clinvar	1 clinvar		26
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	25	1	1	27

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138960.4	RefSeq	NP_620410.3	1	MANE Select
ENST00000283891.6	Ensembl	ENSP00000355119.4	1	MANE Select
ENST00000561129.2	Ensembl	ENSP00000453704.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000561129
Coding exons: 1
Length: 1002

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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00373

Gene Damage Prediction

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