NKAIN2

protein-coding

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

Gene summary

This gene encodes a transmembrane protein that interacts with the beta subunit of a sodium/potassium-transporting ATPase. A chromosomal translocation involving this gene is a cause of lymphoma. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]

Previous symbols:

TCBA1

MANE transcript

NM_001040214.3

Inheritance

—

ClinVar variants

U:20B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr6:123,803,865-124,825,640

External References & Databases

Ensembl (ENSG00000188580)

Transcript & Mutation Effects

hg38 • Region Span ~1,021.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NKAIN2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 19

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001040214.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			20 clinvar			20
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	20	0	1	21

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001040214.3	RefSeq	NP_001035304.1	7	MANE Select
ENST00000368417.6	Ensembl	ENSP00000357402.1	7	MANE Select
NM_001300737.2	RefSeq	NP_001287666.1	7	Standard
NM_001300738.2	RefSeq	NP_001287667.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of sodium ion transport

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368417
Coding exons: 7
Length: 1021518
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125743
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.02	88	119	0.738	0.00000612	1350
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.624
RVIS EVS: -0.16
RVIS percentile EVS: 41.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.432

Gene Damage Prediction

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