NKAIN4

protein-coding

sodium/potassium transporting ATPase interacting 4, the group of Na+/K+ transporting ATPase interacting

Gene summary

NKAIN4 is a member of a family of mammalian proteins (see NKAIN1; MIM 612871) with similarity to Drosophila Nkain and interacts with the beta subunit of Na,K-ATPase (ATP1B1; MIM 182330) (Gorokhova et al., 2007 [PubMed 17606467]).[supplied by OMIM, Jun 2009]

Previous symbols:

C20orf58

MANE transcript

NM_152864.4

Inheritance

—

ClinVar variants

U:44B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr20:63,240,784-63,272,694

External References & Databases

Ensembl (ENSG00000101198)

Transcript & Mutation Effects

hg38 • Region Span ~31.9 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 NKAIN4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 47

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152864.4. 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						0
missense			43 clinvar	5 clinvar		48
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	44	5	0	49

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152864.4	RefSeq	NP_690603.3	7	MANE Select
ENST00000370316.8	Ensembl	ENSP00000359340.3	7	MANE Select
NM_001363718.1	RefSeq	NP_001350647.1	5	Standard
NM_001363747.1	RefSeq	NP_001350676.1	6	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: ENST00000370316
Coding exons: 7
Length: 31911
Individuals with no LoFs: 125716
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125739
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0623	110	108	1.02	0.00000655	1315
Missense (PolyPhen)		37	36.115	1.0245		493
Synonymous	0.692	41	47.0	0.872	0.00000299	417
Loss of Function	1.60	5	10.6	0.470	4.54e-7	131

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000054	0.000053	rare
South Asian	0.00047	0.00042	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.681
RVIS EVS: 1.1
RVIS percentile EVS: 91.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0756

Gene Damage Prediction

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