NIFK

nucleolar protein interacting with the FHA domain of MKI67, the group of RNA binding motif containing

Basic information

Region (hg38): 2:121726945-121736911

Previous symbols: [ "MKI67IP" ]

Links

ENSG00000155438 ∙ NCBI:84365 ∙ OMIM:611970 ∙ HGNC:17838 ∙ Uniprot:Q9BYG3 ∙ 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 NIFK gene.

• not_specified (31 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIFK gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032390.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			29	2		31
nonsense						0
start loss						0
frameshift				1		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	29	3	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIFK	protein_coding	protein_coding	ENST00000285814	7	9979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000278	0.941	125528	0	216	125744	0.000859

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.567	181	161	1.13	0.00000878	1906
Missense in Polyphen		26	27.239	0.9545		354
Synonymous	-0.824	64	56.1	1.14	0.00000267	550
Loss of Function	1.69	8	15.1	0.530	8.05e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000369	0.000368
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.00361	0.00361
European (Non-Finnish)	0.00106	0.00106
Middle Eastern	0.000165	0.000163
South Asian	0.0000653	0.0000653
Other	0.000664	0.000652

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0942

Intolerance Scores

• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.348
• hipred: Y
• hipred_score: 0.536
• ghis: 0.631

Essentials

• essential_gene_gene_trap: E

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nifk

Zebrafish Information Network

• Gene name: nifk
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: necrotic

Gene ontology

• Biological process: rRNA transcription;rRNA metabolic process;protein-containing complex assembly
• Cellular component: condensed nuclear chromosome;nucleoplasm;nucleolus;cytoplasm
• Molecular function: RNA binding;protein binding