NKAIN2

sodium/potassium transporting ATPase interacting 2, the group of Na+/K+ transporting ATPase interacting

Basic information

Region (hg38): 6:123803864-124825640

Previous symbols: [ "TCBA1" ]

Links

ENSG00000188580 ∙ NCBI:154215 ∙ OMIM:609758 ∙ HGNC:16443 ∙ Uniprot:Q5VXU1 ∙ 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 NKAIN2 gene.

• Inborn genetic diseases (7 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NKAIN2 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	7	1	1

Variants in NKAIN2

This is a list of pathogenic ClinVar variants found in the NKAIN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-123804213-A-G		not specified	Uncertain significance (Dec 13, 2022)
6-123804242-T-G		not specified	Uncertain significance (Jul 05, 2023)
6-124283055-A-G			Benign (Dec 31, 2019)
6-124283083-A-G		not specified	Uncertain significance (Apr 26, 2023)
6-124283123-G-A		not specified	Uncertain significance (Mar 07, 2024)
6-124283138-C-A		not specified	Uncertain significance (May 28, 2023)
6-124658384-G-A		not specified	Uncertain significance (Apr 27, 2022)
6-124791376-G-C		not specified	Uncertain significance (Sep 27, 2021)
6-124818398-G-T		not specified	Uncertain significance (Jun 24, 2022)
6-124818478-T-C			Likely benign (May 30, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NKAIN2	protein_coding	protein_coding	ENST00000368417	7	1021518

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0237	0.964	125734	0	9	125743	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	88	119	0.738	0.00000612	1350
Missense in Polyphen		25	44.977	0.55584		535
Synonymous	-0.176	44	42.5	1.03	0.00000243	386
Loss of Function	2.18	5	13.7	0.365	6.66e-7	154

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.000164	0.000163
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.624
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.356
• hipred: N
• hipred_score: 0.263
• ghis: 0.576

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.432

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nkain2

Gene ontology

• Biological process: regulation of sodium ion transport
• Cellular component: plasma membrane;integral component of membrane