TGIF2LY

protein-coding

TGFB induced factor homeobox 2 like Y-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. 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. The C-terminus of this protein is divergent from that of its chromosome X homolog (TGIF2LX), suggesting that this protein may act as a regulator of TGIF2LX. [provided by RefSeq, Jul 2008]

MANE transcript

NM_139214.3

Inheritance

—

ClinVar variants

P:1

Top phenotype

Male infertility with azoospermia or oligozoospermia due to single gene mutation

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chrY:3,579,067-3,580,041

External References & Databases

Ensembl (ENSG00000176679)

Transcript & Mutation Effects

hg38 • Region Span ~1.0 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 TGIF2LY variants in ClinVar

1 Conditions Cataloged

Male infertility with azoospermia or oligozoospermia due to single gene mutationTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_139214.3. 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						0
nonsense						0
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)						0
Total	0	1	0	0	0	1

Highest pathogenic variant AF is 0.0004979967

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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_139214.3	RefSeq	NP_631960.1	1	MANE Select
ENST00000321217.5	Ensembl	ENSP00000318502.4	1	MANE Select
ENST00000559055.2	Ensembl	ENSP00000453750.1	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
protein binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000321217
Coding exons: 1
Length: 1001

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.279	46	41.0	1.12	0.00000764	1211
Missense (PolyPhen)		16	11.911	1.3433		333
Synonymous	-0.407	20	17.8	1.12	0.00000348	366
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. May act as a competitor/regulator of TGIF2LX.;

Essentials

Essential (CRISPR): N
Indispensability pred.: N
Indispensability score: 0.185