POMZP3

protein-coding

POM121 and ZP3 fusion

Gene summary

This gene appears to have resulted from a fusion of DNA sequences derived from 2 distinct loci, specifically through the duplication of two internal exons from the POM121 gene and four 3' exons from the ZP3 gene. The 5' end of this gene is similar to the 5` coding region of the POM121 gene which encodes an integral nuclear pore membrane protein. However, the protein encoded by this gene lacks the nuclear pore localization motif. The 3' end of this gene is similar to the last 4 exons of the zona pellucida glycoprotein 3 (ZP3) gene and the encoded protein retains one zona pellucida domain. Multiple protein isoforms are encoded by transcript variants of this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_012230.5

Inheritance

—

ClinVar variants

U:32B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr7:76,609,986-76,627,279

External References & Databases

Ensembl (ENSG00000146707)

Transcript & Mutation Effects

hg38 • Region Span ~17.3 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 POMZP3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 27

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012230.5. 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			29 clinvar			29
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	32	1	0	33

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012230.5	RefSeq	NP_036362.3	5	MANE Select
ENST00000310842.9	Ensembl	ENSP00000309233.4	5	MANE Select
NM_152992.4	RefSeq	NP_694537.1	4	Standard
ENST00000275569.8	Ensembl	ENSP00000275569.4	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

binding of sperm to zona pellucida
biological_process
egg coat formation
positive regulation of acrosome reaction

Molecular Function

molecular_function
acrosin binding
structural constituent of egg coat

Cellular Component

cellular_component
nucleoplasm
nuclear membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000310842
Coding exons: 5
Length: 17276
Individuals with no LoFs: 51852
Homozygous LoFs: 28758
Heterozygous LoFs: 45138
Defined: 125748
p: 0.358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.461	116	103	1.13	0.00000549	1213
Missense (PolyPhen)		25	25.102	0.99592		315
Synonymous	-1.95	56	40.2	1.39	0.00000231	359
Loss of Function	0.861	6	8.75	0.686	4.38e-7	103

Population LoF Frequency

Population	CAF	p-value	Status
African	0.55	0.41	notable
Latino/Admixed American	0.47	0.35	notable
Ashkenazi Jewish	0.59	0.35	notable
East Asian	0.43	0.37	notable
Finnish	0.34	0.28	notable
European (Non-Finnish)	0.50	0.36	notable
South Asian	0.54	0.37	notable
Other	0.50	0.36	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0865

Intolerance Scores

LoFtool: 0.579
RVIS EVS: 0.42
RVIS percentile EVS: 76.81

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0553

Gene Damage Prediction

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