NIF3L1

NGG1 interacting factor 3 like 1

Basic information

Region (hg38): 2:200889326-200903938

Previous symbols: [ "ALS2CR1" ]

Links

ENSG00000196290 ∙ NCBI:60491 ∙ OMIM:605778 ∙ HGNC:13390 ∙ Uniprot:Q9GZT8 ∙ 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 NIF3L1 gene.

• Inborn genetic diseases (20 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIF3L1 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	18	2	1

Variants in NIF3L1

This is a list of pathogenic ClinVar variants found in the NIF3L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-200891952-A-G			Benign (Jan 03, 2019)
2-200891959-G-A		not specified	Uncertain significance (Dec 02, 2022)
2-200891975-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-200891984-G-A		not specified	Likely benign (Dec 19, 2022)
2-200892016-C-T		not specified	Uncertain significance (Aug 15, 2023)
2-200892053-T-C		not specified	Uncertain significance (Oct 22, 2021)
2-200892149-T-C		not specified	Uncertain significance (Sep 14, 2022)
2-200892204-C-A		not specified	Uncertain significance (Sep 13, 2023)
2-200892229-A-G		not specified	Uncertain significance (May 09, 2023)
2-200892248-G-A		not specified	Likely benign (Jun 02, 2023)
2-200892280-G-C		not specified	Uncertain significance (Apr 03, 2023)
2-200892287-G-A		not specified	Likely benign (Feb 14, 2024)
2-200892319-C-G		not specified	Uncertain significance (Dec 19, 2022)
2-200892326-C-T		not specified	Uncertain significance (Mar 08, 2024)
2-200892350-G-A		not specified	Uncertain significance (Oct 05, 2023)
2-200893279-A-G		not specified	Uncertain significance (Nov 18, 2023)
2-200893289-C-G		not specified	Uncertain significance (Dec 13, 2022)
2-200895317-T-G		not specified	Uncertain significance (Jul 06, 2021)
2-200895343-C-T		not specified	Uncertain significance (Jun 06, 2023)
2-200897076-C-T		not specified	Uncertain significance (Jul 09, 2021)
2-200897146-T-C		not specified	Uncertain significance (Oct 06, 2022)
2-200897152-G-A		not specified	Uncertain significance (Mar 04, 2024)
2-200899388-C-G		not specified	Uncertain significance (Dec 08, 2021)
2-200899402-G-A		not specified	Uncertain significance (May 31, 2023)
2-200899430-G-T		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIF3L1	protein_coding	protein_coding	ENST00000409020	6	14606

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.72e-9	0.312	124681	0	116	124797	0.000465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.219	226	217	1.04	0.0000124	2444
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00127	0.00127
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000111	0.000111
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000601	0.000600
Middle Eastern	0.000111	0.000111
South Asian	0.000197	0.000196
Other	0.000495	0.000495

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0452
• hipred: N
• hipred_score: 0.169
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.843

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nif3l1

Gene ontology

• Biological process: neuron differentiation;positive regulation of transcription, DNA-templated;negative regulation of nucleic acid-templated transcription
• Cellular component: nucleus;cytoplasm;mitochondrion
• Molecular function: protein binding;transcription factor binding;identical protein binding