GARIN3

protein-coding

golgi associated RAB2B interactor family member 3

Gene summary

Predicted to act upstream of or within several processes, including acrosome assembly; binding activity of sperm to zona pellucida; and penetration of zona pellucida. Located in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

FAM71B

MANE transcript

NM_130899.3

Inheritance

—

ClinVar variants

U:108B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr5:157,161,846-157,166,264

External References & Databases

Ensembl (ENSG00000170613)

Transcript & Mutation Effects

hg38 • Region Span ~4.4 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 GARIN3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 120

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_130899.3. 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				1 clinvar		1
missense			108 clinvar	13 clinvar		121
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	108	14	0	122

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_130899.3	RefSeq	NP_570969.2	2	MANE Select
ENST00000302938.4	Ensembl	ENSP00000305596.4	2	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000302938
Coding exons: 2
Length: 4419
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125747
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0585	333	336	0.991	0.0000196	3942
Missense (PolyPhen)		55	69.105	0.79589		926
Synonymous	-0.0802	133	132	1.01	0.00000839	1245
Loss of Function	0.957	5	7.90	0.633	5.22e-7	87

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in RNA biogenesis. {ECO:0000269|PubMed:17103222}.;

Recessive Scores

pRec: 0.0742

Intolerance Scores

LoFtool: 0.641
RVIS EVS: 0.49
RVIS percentile EVS: 79.55

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0500

Gene Damage Prediction

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