NAIF1

protein-coding

nuclear apoptosis inducing factor 1

Gene summary

Involved in negative regulation of cell growth and regulation of mitochondrial membrane permeability involved in apoptotic process. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C9orf90

MANE transcript

NM_197956.4

Inheritance

—

ClinVar variants

U:39B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr9:128,061,233-128,068,206

External References & Databases

Ensembl (ENSG00000171169)

Transcript & Mutation Effects

hg38 • Region Span ~7.0 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 NAIF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 38

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_197956.4. 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			1 clinvar	1 clinvar		2
missense			38 clinvar			38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	39	1	0	40

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_197956.4	RefSeq	NP_931045.1	2	MANE Select
ENST00000373078.5	Ensembl	ENSP00000362170.4	2	MANE Select
ENST00001118447.1	Ensembl	ENSP00000788252.1	2	Standard
ENST00001140749.1	Ensembl	ENSP00000810163.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of cell growth
regulation of mitochondrial membrane permeability involved in apoptotic process

Molecular Function

molecular_function
protein binding

Cellular Component

nucleus
nucleoplasm
mitochondrion
cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373078
Coding exons: 2
Length: 6974
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125744
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.17	127	217	0.585	0.0000150	2086
Missense (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

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	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.990

Gene Damage Prediction

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