NIPA2

protein-coding

NIPA magnesium transporter 2, the group of Solute carrier family 57, NIPA-like magnesium transporters

Gene summary

This gene encodes a possible magnesium transporter. This gene is located adjacent to the imprinted domain in the Prader-Willi syndrome deletion region of chromosome 15. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 3, 7 and 21.[provided by RefSeq, May 2010]

MANE transcript

NM_030922.7

Inheritance

—

ClinVar variants

P:1U:58B:18

Top phenotype

NIPA2-related disorder

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr15:22,838,644-22,869,362

External References & Databases

Ensembl (ENSG00000140157)

Transcript & Mutation Effects

hg38 • Region Span ~30.7 kb

Loading mutation effect viewer...

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 NIPA2 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 61

not providedTotal: 8

NIPA2-related disorderTotal: 7

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030922.7. 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	12 clinvar		13
missense		1 clinvar	53 clinvar	5 clinvar	1 clinvar	60
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	1	58	17	1	77

Highest pathogenic variant AF is 0.000059486705

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 349 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030922.7	RefSeq	NP_112184.4	5	MANE Select
ENST00000337451.8	Ensembl	ENSP00000337618.3	5	MANE Select
NM_001008860.3	RefSeq	NP_001008860.1	5	Standard
NM_001008892.3	RefSeq	NP_001008892.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Prader-Willi and Angelman Syndrome
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

early endosome
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000337451
Coding exons: 5
Length: 29744
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125748
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.223	187	196	0.955	0.0000101	2335
Missense (PolyPhen)		46	64.523	0.71292		842
Synonymous	-2.11	99	75.6	1.31	0.00000433	745
Loss of Function	3.02	1	12.5	0.0798	6.59e-7	157

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00052	0.00052	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000053	0.000044	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a selective Mg(2+) transporter. {ECO:0000250}.;

Recessive Scores

pRec: 0.122

Intolerance Scores

LoFtool: 0.0536
RVIS EVS: -0.03
RVIS percentile EVS: 51.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.207

Gene Damage Prediction

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