NIPAL3

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

Basic information

Region (hg38): 1:24415802-24475252

Previous symbols: [ "NPAL3" ]

Links

ENSG00000001461 ∙ NCBI:57185 ∙ OMIM:620034 ∙ HGNC:25233 ∙ Uniprot:Q6P499 ∙ 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 NIPAL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIPAL3 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				1		1
missense			35	1		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	37	2	0

Variants in NIPAL3

This is a list of pathogenic ClinVar variants found in the NIPAL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-24415834-C-T		NIPAL3-related disorder	Benign (Jul 25, 2019)
1-24419565-C-A		not specified	Uncertain significance (Mar 07, 2024)
1-24419566-G-A		NIPAL3-related disorder	Benign (Jun 12, 2019)
1-24419614-G-A		not specified	Uncertain significance (Nov 15, 2024)
1-24419637-C-T		NIPAL3-related disorder	Benign (Nov 16, 2019)
1-24440173-A-C		not specified	Uncertain significance (Feb 27, 2023)
1-24440214-G-A		not specified	Uncertain significance (Apr 12, 2024)
1-24442070-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-24442074-T-C		not specified	Uncertain significance (Mar 18, 2024)
1-24442097-G-A		Neurodevelopmental disorder	Uncertain significance (Jan 01, 2019)
1-24442113-A-G		not specified	Uncertain significance (May 11, 2022)
1-24442145-C-G		not specified	Uncertain significance (Jul 07, 2024)
1-24442160-G-A		not specified	Uncertain significance (Jun 02, 2023)
1-24442175-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-24442196-A-T		not specified	Uncertain significance (Aug 14, 2024)
1-24442221-T-A		not specified	Uncertain significance (May 23, 2023)
1-24445230-C-T		not specified	Uncertain significance (Sep 27, 2021)
1-24445231-G-A			Likely benign (Nov 01, 2022)
1-24449483-C-T		not specified	Uncertain significance (Mar 06, 2025)
1-24449564-G-A		not specified	Uncertain significance (Dec 14, 2024)
1-24449576-G-A		not specified	Uncertain significance (Jan 04, 2022)
1-24449609-C-T		not specified	Uncertain significance (Feb 14, 2023)
1-24449624-A-G		not specified	Uncertain significance (May 15, 2024)
1-24453420-A-G		not specified	Likely benign (Oct 12, 2021)
1-24453420-A-T		not specified	Uncertain significance (Jan 17, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIPAL3	protein_coding	protein_coding	ENST00000374399	11	57183

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000696	0.980	125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.675	218	248	0.879	0.0000146	2650
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000968	0.0000968
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000944	0.0000924
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000163	0.000163
South Asian	0.0000654	0.0000653
Other	0.000352	0.000326

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.232
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.33

Haploinsufficiency Scores

• pHI: 0.269
• hipred: N
• hipred_score: 0.394
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.617

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nipal3
• Phenotype: respiratory system phenotype; immune system phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

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