NIPAL2

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

Basic information

Region (hg38): 8:98189826-98294393

Previous symbols: [ "NPAL2" ]

Links

ENSG00000104361 ∙ NCBI:79815 ∙ ∙ HGNC:25854 ∙ Uniprot:Q9H841 ∙ 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 NIPAL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIPAL2 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						0
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in NIPAL2

This is a list of pathogenic ClinVar variants found in the NIPAL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-98195993-T-C		not specified	Uncertain significance (Sep 27, 2021)
8-98203195-A-G		not specified	Uncertain significance (Jun 30, 2023)
8-98205129-G-C		not specified	Uncertain significance (Jun 17, 2024)
8-98205149-C-T		not specified	Uncertain significance (Dec 12, 2023)
8-98205206-C-A		not specified	Uncertain significance (Feb 28, 2023)
8-98205217-C-T		not specified	Uncertain significance (Dec 06, 2021)
8-98212444-T-C		not specified	Uncertain significance (Jan 26, 2022)
8-98212477-T-C		not specified	Uncertain significance (Jan 30, 2024)
8-98222579-C-A		not specified	Uncertain significance (Jun 07, 2024)
8-98252490-C-T		not specified	Uncertain significance (May 11, 2022)
8-98252537-T-C		not specified	Uncertain significance (Feb 06, 2023)
8-98252564-C-T		not specified	Uncertain significance (Aug 23, 2021)
8-98252606-T-C		not specified	Uncertain significance (Mar 23, 2023)
8-98254049-G-C		not specified	Uncertain significance (Nov 21, 2023)
8-98294014-G-T		not specified	Uncertain significance (May 16, 2022)
8-98294025-C-T		not specified	Uncertain significance (Mar 15, 2024)
8-98294037-C-T		not specified	Uncertain significance (Jul 13, 2021)
8-98294038-C-A		not specified	Uncertain significance (Apr 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIPAL2	protein_coding	protein_coding	ENST00000341166	12	104561

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.37e-12	0.0522	26927	37563	61258	125748	0.537

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.810	149	180	0.830	0.00000870	2352
Missense in Polyphen		49	62.034	0.78989		830
Synonymous	0.748	60	67.8	0.884	0.00000361	728
Loss of Function	0.187	18	18.9	0.954	8.57e-7	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	1.16	1.16
Ashkenazi Jewish	0.559	0.550
East Asian	0.593	0.595
Finnish	0.510	0.509
European (Non-Finnish)	0.496	0.495
Middle Eastern	0.593	0.595
South Asian	0.609	0.601
Other	0.540	0.541

dbNSFP

Source: dbNSFP

• Pathway: Transport of small molecules;Miscellaneous transport and binding events (Consensus)

Intolerance Scores

• loftool: 0.408
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.216
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00412

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nipal2

Gene ontology

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