NFIC

nuclear factor I C, the group of Nuclear factor I family

Basic information

Region (hg38): 19:3314403-3469217

Previous symbols: [ "NFI" ]

Links

ENSG00000141905 ∙ NCBI:4782 ∙ OMIM:600729 ∙ HGNC:7786 ∙ Uniprot:P08651 ∙ 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 NFIC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFIC 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			39			39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	0	0

Variants in NFIC

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

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

Position	Type	Phenotype	Significance	ClinVar
19-3381791-G-A		not specified	Uncertain significance (Sep 15, 2021)
19-3381844-C-T		not specified	Uncertain significance (Aug 28, 2023)
19-3381964-A-G		not specified	Uncertain significance (Apr 25, 2022)
19-3381970-A-G		not specified	Uncertain significance (Mar 14, 2023)
19-3381988-G-T		not specified	Uncertain significance (Mar 30, 2024)
19-3382231-G-C		not specified	Uncertain significance (Apr 07, 2023)
19-3382235-G-A		not specified	Uncertain significance (Jan 02, 2025)
19-3382241-G-A		not specified	Uncertain significance (Apr 25, 2022)
19-3425109-C-A		not specified	Uncertain significance (Jul 28, 2021)
19-3425177-G-A		not specified	Uncertain significance (Nov 21, 2024)
19-3433521-C-T		not specified	Uncertain significance (Jul 05, 2023)
19-3433526-G-T		not specified	Uncertain significance (Aug 02, 2022)
19-3433553-G-A		not specified	Uncertain significance (Mar 01, 2023)
19-3433562-A-G		not specified	Uncertain significance (Mar 03, 2025)
19-3433565-G-A		not specified	Uncertain significance (Jul 15, 2021)
19-3434282-G-A		not specified	Uncertain significance (Sep 16, 2021)
19-3434304-A-G		not specified	Uncertain significance (Feb 21, 2025)
19-3434361-C-G		not specified	Uncertain significance (Dec 23, 2024)
19-3435089-G-C		not specified	Uncertain significance (Jan 29, 2024)
19-3435102-G-C		not specified	Uncertain significance (Dec 19, 2023)
19-3435139-G-A		not specified	Uncertain significance (May 04, 2023)
19-3435143-T-G		not specified	Uncertain significance (Jan 29, 2025)
19-3435195-G-A		not specified	Uncertain significance (Sep 27, 2022)
19-3435198-A-G		not specified	Uncertain significance (Sep 26, 2022)
19-3449068-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NFIC	protein_coding	protein_coding	ENST00000443272	11	109655

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0905	0.909	125734	0	10	125744	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.06	233	340	0.686	0.0000250	3254
Missense in Polyphen		82	150.14	0.54615		1388
Synonymous	-0.882	173	159	1.09	0.0000131	1045
Loss of Function	3.14	6	21.8	0.275	0.00000102	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.000382	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000273	0.0000264
Middle Eastern	0.000382	0.000326
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Recognizes and binds the palindromic sequence 5'- TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.
• Pathway: Gene expression (Transcription);RNA Polymerase III Transcription Termination;FOXA1 transcription factor network;RNA Polymerase III Abortive And Retractive Initiation;RNA Polymerase III Transcription (Consensus)

Recessive Scores

• pRec: 0.617

Intolerance Scores

• loftool: 0.245
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.86

Haploinsufficiency Scores

• pHI: 0.457
• hipred: Y
• hipred_score: 0.774
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.875

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nfic
• Phenotype: craniofacial phenotype; growth/size/body region phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;DNA replication;transcription by RNA polymerase II;odontogenesis of dentin-containing tooth;positive regulation of transcription by RNA polymerase II
• Cellular component: fibrillar center;nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity