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.

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.

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			15			15
nonsense						0
start loss			1			1
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in NIFK

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

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

Position	Type	Phenotype	Significance	ClinVar
2-121727743-C-T		not specified	Uncertain significance (Mar 15, 2024)
2-121727801-A-C		not specified	Likely benign (Jun 30, 2024)
2-121727837-T-C		not specified	Uncertain significance (Nov 29, 2023)
2-121727863-T-TGA			Likely benign (Sep 03, 2018)
2-121727872-C-T		not specified	Uncertain significance (Mar 25, 2024)
2-121727890-G-A		not specified	Uncertain significance (Jul 08, 2022)
2-121728329-A-C		not specified	Uncertain significance (Jan 06, 2023)
2-121728349-C-A		not specified	Uncertain significance (Jan 03, 2024)
2-121728349-C-T		not specified	Uncertain significance (May 27, 2022)
2-121728350-G-A		not specified	Uncertain significance (Oct 05, 2023)
2-121728493-G-A		not specified	Uncertain significance (Dec 16, 2023)
2-121730897-G-A		not specified	Uncertain significance (Sep 14, 2023)
2-121730976-T-A		not specified	Uncertain significance (Mar 01, 2024)
2-121730999-C-T		not specified	Uncertain significance (Jun 24, 2022)
2-121731014-C-T		not specified	Uncertain significance (Jun 07, 2023)
2-121731016-T-A		not specified	Uncertain significance (May 10, 2023)
2-121731093-G-A		not specified	Uncertain significance (Jun 11, 2024)
2-121732131-A-G		not specified	Uncertain significance (Feb 28, 2024)
2-121732197-T-C		not specified	Uncertain significance (Jun 17, 2024)
2-121735680-G-C		not specified	Uncertain significance (May 31, 2023)
2-121735713-T-C		not specified	Uncertain significance (Nov 21, 2024)
2-121736767-C-A		not specified	Uncertain significance (Jul 27, 2024)
2-121736788-C-G		not specified	Uncertain significance (Sep 01, 2021)
2-121736837-G-A		not specified	Uncertain significance (Jan 18, 2022)

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