NFX1

nuclear transcription factor, X-box binding 1, the group of Ring finger proteins|PHD finger proteins

Basic information

Region (hg38): 9:33290512-33371157

Links

ENSG00000086102 ∙ ∙ OMIM:603255 ∙ HGNC:7803 ∙ Uniprot:Q12986 ∙ 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 NFX1 gene.

• not_specified (112 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002504.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			107	5		112
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	107	7	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NFX1	protein_coding	protein_coding	ENST00000379540	24	80647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000115	1.00	125701	1	46	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	520	619	0.840	0.0000327	7415
Missense in Polyphen		116	181.35	0.63965		1967
Synonymous	0.665	206	219	0.943	0.0000120	2032
Loss of Function	4.99	19	61.1	0.311	0.00000337	756

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000662	0.000662
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000158	0.000149
Middle Eastern	0.000109	0.000109
South Asian	0.000262	0.000261
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to the X-box motif of MHC class II genes and represses their expression. May play an important role in regulating the duration of an inflammatory response by limiting the period in which MHC class II molecules are induced by interferon-gamma. Isoform 3 binds to the X-box motif of TERT promoter and represses its expression. Together with PABPC1 or PABPC4, isoform 1 acts as a coactivator for TERT expression. Mediates E2-dependent ubiquitination. {ECO:0000269|PubMed:10500182, ECO:0000269|PubMed:15371341, ECO:0000269|PubMed:17267499}.
• Pathway: Human papillomavirus infection - Homo sapiens (human);Fas Ligand (FasL) pathway and Stress induction of Heat Shock Proteins (HSP) regulation;Tryptophan degradation (Consensus)

Intolerance Scores

• loftool: 0.793
• rvis_EVS: -1.59
• rvis_percentile_EVS: 3.08

Haploinsufficiency Scores

• pHI: 0.440
• hipred: Y
• hipred_score: 0.637
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nfx1

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;inflammatory response;viral process;negative regulation of MHC class II biosynthetic process
• Cellular component: nucleus;nucleolus;cytosol;plasma membrane
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;RNA binding;zinc ion binding;transferase activity