NIPAL1

protein-coding

NIPA like domain containing 1, 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 located in Golgi apparatus. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

NPAL1

MANE transcript

NM_207330.3

Inheritance

—

ClinVar variants

U:42B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr4:47,914,142-48,040,173

External References & Databases

Ensembl (ENSG00000163293)

Transcript & Mutation Effects

hg38 • Region Span ~126.0 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 NIPAL1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 38

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207330.3. 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			40 clinvar	1 clinvar		41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	42	1	0	43

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207330.3	RefSeq	NP_997213.1	6	MANE Select
ENST00000295461.10	Ensembl	ENSP00000295461.5	6	MANE Select
ENST00000511123.1	Ensembl	ENSP00000422276.1	3	Standard
ENST00000511852.5	Ensembl	ENSP00000425795.1	4	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

magnesium ion transmembrane transporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295461
Coding exons: 6
Length: 126030
Individuals with no LoFs: 125670
Homozygous LoFs: 0
Heterozygous LoFs: 77
Defined: 125747
p: 0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.678	179	206	0.867	0.00000921	2634
Missense (PolyPhen)		81	82.018	0.98759		1092
Synonymous	0.826	73	82.5	0.884	0.00000409	840
Loss of Function	0.0859	15	15.4	0.976	6.51e-7	201

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00080	0.00068	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0.00079	0.00079	rare
East Asian	0.00087	0.00087	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00059	0.00059	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a Mg(2+) transporter. Can also transport other divalent cations such as Fe(2+), Sr(2+), Ba(2+), Mn(2+), Cu(2+) and Co(2+) but to a much less extent than Mg(2+) (By similarity). {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.362
RVIS EVS: 0.6
RVIS percentile EVS: 82.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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