NAIF1

nuclear apoptosis inducing factor 1

Basic information

Region (hg38): 9:128061233-128068206

Previous symbols: [ "C9orf90" ]

Links

ENSG00000171169 ∙ NCBI:203245 ∙ OMIM:610673 ∙ HGNC:25446 ∙ Uniprot:Q69YI7 ∙ 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 NAIF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAIF1 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in NAIF1

This is a list of pathogenic ClinVar variants found in the NAIF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128063492-G-A		not specified	Uncertain significance (Jul 27, 2024)
9-128063528-T-C		not specified	Uncertain significance (Mar 11, 2025)
9-128063540-G-A		not specified	Uncertain significance (Jul 14, 2021)
9-128063593-C-A		not specified	Uncertain significance (Sep 16, 2021)
9-128063640-G-A		not specified	Uncertain significance (Apr 08, 2022)
9-128063658-C-T		not specified	Uncertain significance (Feb 11, 2025)
9-128063758-G-A			Likely benign (Dec 01, 2022)
9-128063780-G-A		not specified	Uncertain significance (Apr 05, 2023)
9-128063813-G-C		not specified	Uncertain significance (Jan 30, 2024)
9-128063859-C-G		not specified	Uncertain significance (Jan 25, 2023)
9-128063865-C-T		not specified	Uncertain significance (Dec 22, 2023)
9-128066606-C-G		not specified	Uncertain significance (Jan 30, 2025)
9-128066665-C-T		not specified	Uncertain significance (Nov 08, 2022)
9-128066737-G-C		not specified	Uncertain significance (May 05, 2023)
9-128066798-C-T		not specified	Uncertain significance (May 15, 2024)
9-128066834-C-G		not specified	Uncertain significance (Mar 01, 2025)
9-128066837-C-T		not specified	Uncertain significance (Sep 10, 2024)
9-128066917-C-T		not specified	Uncertain significance (Oct 16, 2023)
9-128066918-G-A		not specified	Uncertain significance (Feb 06, 2025)
9-128066987-C-T		not specified	Uncertain significance (May 02, 2024)
9-128067050-C-T		not specified	Uncertain significance (Oct 25, 2023)
9-128067058-C-G		not specified	Uncertain significance (Aug 20, 2024)
9-128067095-C-A		not specified	Uncertain significance (Dec 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAIF1	protein_coding	protein_coding	ENST00000373078	2	6974

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.286	0.695	125738	0	6	125744	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.17	127	217	0.585	0.0000150	2086
Missense in Polyphen		57	101.46	0.56182		1000
Synonymous	0.354	93	97.5	0.954	0.00000728	715
Loss of Function	1.96	2	7.99	0.250	3.47e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Induces apoptosis. {ECO:0000269|PubMed:16378748}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.0646
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.416
• hipred: Y
• hipred_score: 0.546
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Naif1

Gene ontology

• Biological process: negative regulation of cell growth;regulation of mitochondrial membrane permeability involved in apoptotic process
• Cellular component: nucleus;nucleoplasm;mitochondrion;cytosol;plasma membrane
• Molecular function: molecular_function;protein binding