ZFY

protein-coding

zinc finger protein Y-linked, the group of Zinc fingers C2H2-type

Gene summary

This gene encodes a zinc finger-containing protein that may function as a transcription factor. This gene was once a candidate gene for the testis-determining factor (TDF) and was erroneously referred to as TDF. [provided by RefSeq, Jul 2008]

MANE transcript

NM_003411.4

Inheritance

—

ClinVar variants

U:43

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chrY:2,935,281-2,982,506

External References & Databases

Ensembl (ENSG00000067646)

Transcript & Mutation Effects

hg38 • Region Span ~47.2 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 ZFY variants in ClinVar

0 Conditions Cataloged

No annotated ClinVar phenotypes.

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003411.4. 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			7 clinvar			7
missense			22 clinvar			22
nonsense			5 clinvar			5
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	43	0	0	43

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003411.4	RefSeq	NP_003402.2	7	MANE Select
ENST00000155093.8	Ensembl	ENSP00000155093.3	7	MANE Select
NM_001145275.2	RefSeq	NP_001138747.1	5	Standard
NM_001145276.2	RefSeq	NP_001138748.1	6	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
metal ion binding

Cellular Component

nucleoplasm
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000155093
Coding exons: 7
Length: 47436
Individuals with no LoFs: 61470
Homozygous LoFs: 1
Heterozygous LoFs: 0
Defined: 61471
p: 0.00000813

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.51	84	133	0.631	0.0000199	5421
Missense (PolyPhen)		15	46.968	0.31937		1950
Synonymous	0.0270	46	46.2	0.995	0.00000724	1420
Loss of Function	2.33	1	8.18	0.122	0.00000130	384

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	0.00018	0.000091	rare
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: Probable transcriptional activator. Binds to the consensus sequence 5'-AGGCCY-3'. {ECO:0000269|PubMed:20028140}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.492

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low