NFIC

protein-coding

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

Gene summary

The protein encoded by this gene belongs to the CTF/NF-I family. These are dimeric DNA-binding proteins, and function as cellular transcription factors and as replication factors for adenovirus DNA replication. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Oct 2011]

Previous symbols:

MANE transcript

NM_001245002.2

Inheritance

—

ClinVar variants

U:69

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr19:3,314,403-3,469,217

External References & Databases

Ensembl (ENSG00000141905)

Transcript & Mutation Effects

hg38 • Region Span ~154.8 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 NFIC variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 60

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001245002.2. 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			64 clinvar			64
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	69	0	0	69

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001245002.2	RefSeq	NP_001231931.1	11	MANE Select
ENST00000443272.3	Ensembl	ENSP00000396843.2	11	MANE Select
NM_001245004.2	RefSeq	NP_001231933.1	9	Standard
NM_001245005.2	RefSeq	NP_001231934.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
RNA Polymerase III Transcription Termination
FOXA1 transcription factor network
RNA Polymerase III Abortive And Retractive Initiation
RNA Polymerase III Transcription

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

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

Cellular Component

fibrillar center
nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000443272
Coding exons: 11
Length: 109655
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125744
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.06	233	340	0.686	0.0000250	3254
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00038	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.617

Intolerance Scores

LoFtool: 0.245
RVIS EVS: -0.67
RVIS percentile EVS: 15.86

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.875

Gene Damage Prediction

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