NIPAL3

protein-coding

NIPA like domain containing 3, the group of Solute carrier family 57, NIPA-like magnesium transporters

Gene summary

Predicted to enable magnesium ion transmembrane transporter activity. Predicted to be involved in magnesium ion transport. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

NPAL3

MANE transcript

NM_020448.5

Inheritance

—

ClinVar variants

U:66B:9

Top phenotype

NIPAL3-related disorder

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr1:24,415,802-24,475,252

External References & Databases

Ensembl (ENSG00000001461)

Transcript & Mutation Effects

hg38 • Region Span ~59.5 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 NIPAL3 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 62

NIPAL3-related disorderTotal: 9

not providedTotal: 1

Neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020448.5. 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				4 clinvar	2 clinvar	6
missense			64 clinvar	2 clinvar	1 clinvar	67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	66	6	3	75

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 67 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020448.5	RefSeq	NP_065181.1	11	MANE Select
ENST00000374399.9	Ensembl	ENSP00000363520.4	11	MANE Select
NM_001322854.2	RefSeq	NP_001309783.1	11	Standard
NM_001322855.2	RefSeq	NP_001309784.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Transport of small molecules
Miscellaneous transport and binding events

Biological Process

magnesium ion transport
magnesium ion transmembrane transport

Molecular Function

protein binding
magnesium ion transmembrane transporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374399
Coding exons: 11
Length: 57183
Individuals with no LoFs: 125724
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125747
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.675	218	248	0.879	0.0000146	2650
Missense (PolyPhen)		69	93.276	0.73974		1042
Synonymous	-0.515	116	109	1.06	0.00000793	803
Loss of Function	2.09	10	20.1	0.497	9.53e-7	230

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000035	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000065	0.000065	rare
Other	0.00035	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.232
RVIS EVS: -0.8
RVIS percentile EVS: 12.33

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.617

Gene Damage Prediction

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