NIF3L1

protein-coding

NGG1 interacting factor 3 like 1

Gene summary

Enables RNA polymerase II-specific DNA-binding transcription factor binding activity and identical protein binding activity. Involved in positive regulation of DNA-templated transcription. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ALS2CR1

MANE transcript

NM_001369441.2

Inheritance

—

ClinVar variants

U:62B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr2:200,889,327-200,903,938

External References & Databases

Ensembl (ENSG00000196290)

Transcript & Mutation Effects

hg38 • Region Span ~14.6 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 NIF3L1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 63

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001369441.2. 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				3 clinvar		3
missense			61 clinvar	3 clinvar		64
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	62	6	0	68

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 68 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001369441.2	RefSeq	NP_001356370.1	6	MANE Select
ENST00000409020.6	Ensembl	ENSP00000386394.1	6	MANE Select
NM_001136039.2	RefSeq	NP_001129511.1	6	Standard
NM_001142355.1	RefSeq	NP_001135827.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

neuron differentiation
positive regulation of transcription, DNA-templated
negative regulation of nucleic acid-templated transcription

Molecular Function

protein binding
transcription factor binding
identical protein binding

Cellular Component

nucleus
cytoplasm
mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409020
Coding exons: 6
Length: 14606
Individuals with no LoFs: 124681
Homozygous LoFs: 0
Heterozygous LoFs: 116
Defined: 124797
p: 0.000465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.219	226	217	1.04	0.0000124	2444
Missense (PolyPhen)		78	75.252	1.0365		920
Synonymous	0.960	73	84.2	0.867	0.00000464	790
Loss of Function	0.688	14	17.1	0.820	0.00000113	171

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00052	0.00052	rare
Latino/Admixed American	0.00075	0.00075	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00060	0.00060	rare
South Asian	0.00020	0.00020	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function as a transcriptional corepressor through its interaction with COPS2, negatively regulating the expression of genes involved in neuronal differentiation. {ECO:0000250|UniProtKB:Q9EQ80}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.796
RVIS EVS: -0.38
RVIS percentile EVS: 27.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.843

Gene Damage Prediction

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