EQTN

protein-coding

equatorin

Gene summary

Predicted to be involved in acrosomal vesicle exocytosis; endocytosis; and fusion of sperm to egg plasma membrane involved in single fertilization. Predicted to be located in early endosome and nucleus. Predicted to be active in inner acrosomal membrane; outer acrosomal membrane; and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C9orf11

MANE transcript

NM_020641.3

Inheritance

—

ClinVar variants

U:50B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.35

Max pathogenic AF

—

Genomic locus

chr9:27,284,654-27,297,150

External References & Databases

Ensembl (ENSG00000120160)

Transcript & Mutation Effects

hg38 • Region Span ~12.5 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 EQTN variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 53

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020641.3. 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			50 clinvar	4 clinvar		54
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	4	0	54

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020641.3	RefSeq	NP_065692.2	8	MANE Select
ENST00000380032.8	Ensembl	ENSP00000369371.3	8	MANE Select
NM_001161585.2	RefSeq	NP_001155057.1	7	Standard
ENST00000380031.2	Ensembl	ENSP00000369370.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

endocytosis
fusion of sperm to egg plasma membrane involved in single fertilization
acrosomal vesicle exocytosis

Cellular Component

inner acrosomal membrane
acrosomal membrane
outer acrosomal membrane
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380032
Coding exons: 8
Length: 12482
Individuals with no LoFs: 125673
Homozygous LoFs: 0
Heterozygous LoFs: 69
Defined: 125742
p: 0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.346	163	151	1.08	0.00000722	1939
Missense (PolyPhen)		44	37.403	1.1764		503
Synonymous	0.207	54	56.0	0.965	0.00000302	545
Loss of Function	-1.08	15	11.1	1.35	4.68e-7	153

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000034	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00059	0.00056	rare
South Asian	0.00010	0.000098	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acrosomal membrane-anchored protein involved in the process of fertilization and in acrosome biogenesis. {ECO:0000250}.;

Recessive Scores

pRec: 0.0638

Intolerance Scores

RVIS EVS: 0.08
RVIS percentile EVS: 60.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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