NIPA2

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

Basic information

Region (hg38): 15:22838643-22869362

Links

ENSG00000140157 ∙ NCBI:81614 ∙ OMIM:608146 ∙ HGNC:17044 ∙ Uniprot:Q8N8Q9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NIPA2 gene.

• not provided (27 variants)
• Inborn genetic diseases (12 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIPA2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense		1	13	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					20	20
Total	0	1	13	2	23

Highest pathogenic variant AF is 0.0000526

Variants in NIPA2

This is a list of pathogenic ClinVar variants found in the NIPA2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-22851338-T-C			Benign (Jun 20, 2021)
15-22851396-T-G			Benign (May 14, 2021)
15-22851553-G-A			Benign (May 14, 2021)
15-22851674-C-T			Benign (May 13, 2021)
15-22851729-G-A		NIPA2-related disorder	Benign (Jul 12, 2019)
15-22851783-A-G		not specified	Uncertain significance (Jun 06, 2023)
15-22851830-G-A		NIPA2-related disorder	Benign (May 04, 2021)
15-22851841-G-A		not specified	Uncertain significance (Jul 08, 2022)
15-22851955-C-T			Benign (Nov 12, 2018)
15-22853216-A-T		not specified	Uncertain significance (Aug 08, 2023)
15-22853374-CT-C			Benign (Aug 20, 2019)
15-22853374-CTT-C			Benign (May 13, 2021)
15-22853459-C-T			Benign (May 15, 2021)
15-22853498-C-T			Benign (Jun 20, 2021)
15-22853499-A-G			Benign (Nov 12, 2018)
15-22858257-A-G			Benign (Aug 20, 2019)
15-22858272-C-T			Benign (Nov 12, 2018)
15-22858387-C-G			Benign (May 13, 2021)
15-22858576-C-T		not specified	Uncertain significance (Mar 02, 2023)
15-22858577-G-A		NIPA2-related disorder	Likely benign (Mar 01, 2019)
15-22860320-T-C			Benign (Aug 20, 2019)
15-22860655-A-G		not specified	Uncertain significance (Jul 05, 2023)
15-22860680-A-G		NIPA2-related disorder	Likely benign (May 01, 2019)
15-22860688-G-C		not specified	Uncertain significance (Feb 23, 2023)
15-22865961-C-T			Benign (Nov 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIPA2	protein_coding	protein_coding	ENST00000337451	5	29744

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.921	0.0791	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.223	187	196	0.955	0.0000101	2335
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000644	0.000644
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000439
Middle Eastern	0.000163	0.000163
South Asian	0.0000657	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a selective Mg(2+) transporter. {ECO:0000250}.
• Pathway: Prader-Willi and Angelman Syndrome;Transport of small molecules;Miscellaneous transport and binding events (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.0536
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.191
• hipred: Y
• hipred_score: 0.547
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.207

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nipa2

Gene ontology

• Biological process: magnesium ion transport;magnesium ion transmembrane transport
• Cellular component: early endosome;plasma membrane;integral component of membrane
• Molecular function: magnesium ion transmembrane transporter activity