NIPAL1

NIPA like domain containing 1, the group of Solute carrier family 57, NIPA-like magnesium transporters

Basic information

Region (hg38): 4:47914142-48040173

Previous symbols: [ "NPAL1" ]

Links

ENSG00000163293 ∙ NCBI:152519 ∙ ∙ HGNC:27194 ∙ Uniprot:Q6NVV3 ∙ 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 NIPAL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIPAL1 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 NIPAL1

This is a list of pathogenic ClinVar variants found in the NIPAL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-47936047-AAT-A		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
4-47936069-G-A		Retinitis pigmentosa	Uncertain significance (Apr 27, 2017)
4-47936079-A-G		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
4-47936147-G-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
4-47936147-G-GT		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
4-47936194-T-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
4-47936359-T-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
4-47936368-T-C		Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)
4-47936386-G-A		Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)
4-47936431-T-A			Uncertain significance (Mar 19, 2022)
4-47936432-C-T			Uncertain significance (Oct 17, 2022)
4-47936433-G-A			Likely benign (Sep 08, 2022)
4-47936433-G-T			Likely benign (Oct 13, 2023)
4-47936435-T-G			Uncertain significance (Mar 04, 2022)
4-47936436-G-C			Likely benign (May 30, 2022)
4-47936440-C-G		Retinal dystrophy	Uncertain significance (Oct 01, 2023)
4-47936448-C-T		Retinitis pigmentosa	Benign/Likely benign (Jan 29, 2024)
4-47936449-G-A		Inborn genetic diseases	Likely benign (Nov 07, 2022)
4-47936464-A-G		Inborn genetic diseases	Uncertain significance (Nov 18, 2022)
4-47936479-G-A			Uncertain significance (Feb 12, 2021)
4-47936488-A-G		Retinal dystrophy	Uncertain significance (Oct 01, 2023)
4-47936491-G-A			Uncertain significance (Jun 13, 2022)
4-47936491-G-T			Uncertain significance (Mar 05, 2020)
4-47936492-G-T			Uncertain significance (Aug 27, 2021)
4-47936498-G-A			Likely benign (May 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIPAL1	protein_coding	protein_coding	ENST00000295461	6	126030

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.45e-10	0.0775	125670	0	77	125747	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.678	179	206	0.867	0.00000921	2634
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000861	0.000736
Ashkenazi Jewish	0.000794	0.000794
East Asian	0.000870	0.000870
Finnish	0.00	0.00
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000870	0.000870
South Asian	0.000588	0.000588
Other	0.000163	0.000163

dbNSFP

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

Intolerance Scores

• loftool: 0.362
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.322
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nipal1

Gene ontology

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