GARIN5A

protein-coding

golgi associated RAB2 interactor 5A

Gene summary

Predicted to be involved in defense response to virus; innate immune response; and positive regulation of type I interferon production. Predicted to act upstream of or within several processes, including flagellated sperm motility; penetration of zona pellucida; and spermatid development. Predicted to be located in Golgi apparatus. Predicted to be active in sperm head. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FAM71E1

MANE transcript

NM_001308429.2

Inheritance

—

ClinVar variants

P:2U:52B:3

Top phenotype

Neurodevelopmental disorder with dysmorphic facies and variable seizures

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr19:50,466,785-50,476,848

External References & Databases

Ensembl (ENSG00000142530)

Transcript & Mutation Effects

hg38 • Region Span ~10.1 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 GARIN5A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 50

not providedTotal: 3

Neurodevelopmental disorder with dysmorphic facies and variable seizuresTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001308429.2. 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	2 clinvar		3
missense			51 clinvar	1 clinvar		52
nonsense						0
start loss		1 clinvar				1
frameshift						0
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	0	2	52	3	0	57

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001308429.2	RefSeq	NP_001295358.1	4	MANE Select
ENST00000600100.6	Ensembl	ENSP00000472421.2	4	MANE Select
NM_138411.3	RefSeq	NP_612420.1	4	Standard
ENST00000593796.5	Ensembl	ENSP00000471374.1	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000595790
Coding exons: 4
Length: 9969
Individuals with no LoFs: 125427
Homozygous LoFs: 2
Heterozygous LoFs: 227
Defined: 125656
p: 0.000912

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0369	158	157	1.01	0.0000105	1447
Missense (PolyPhen)		45	57.075	0.78844		536
Synonymous	0.309	64	67.2	0.952	0.00000442	502
Loss of Function	0.448	6	7.31	0.821	3.10e-7	86

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00056	0.00055	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00080	0.00079	rare
East Asian	0.000054	0.000054	rare
Finnish	0.00037	0.00037	rare
European (Non-Finnish)	0.0017	0.0017	notable
South Asian	0.000067	0.000065	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.714
RVIS EVS: 0.19
RVIS percentile EVS: 67.03

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.260

Gene Damage Prediction

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