NFX1
Basic information
Region (hg38): 9:33290511-33371157
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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.
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 | |||||
missense | 44 | 47 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 44 | 4 | 0 |
Variants in NFX1
This is a list of pathogenic ClinVar variants found in the NFX1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
9-33290588-C-A | not specified | Uncertain significance (Nov 30, 2021) | ||
9-33294428-A-G | not specified | Uncertain significance (Feb 12, 2024) | ||
9-33294454-C-G | not specified | Uncertain significance (Sep 29, 2023) | ||
9-33294519-G-A | not specified | Uncertain significance (Apr 08, 2024) | ||
9-33294528-G-C | not specified | Uncertain significance (May 27, 2022) | ||
9-33294534-A-C | not specified | Uncertain significance (Nov 18, 2022) | ||
9-33294536-T-C | not specified | Uncertain significance (Apr 01, 2024) | ||
9-33294546-C-T | not specified | Uncertain significance (Feb 13, 2024) | ||
9-33294551-C-T | not specified | Uncertain significance (Mar 01, 2023) | ||
9-33294596-G-C | not specified | Uncertain significance (Feb 06, 2023) | ||
9-33294618-C-T | not specified | Uncertain significance (Aug 12, 2021) | ||
9-33294638-A-C | not specified | Uncertain significance (Oct 19, 2021) | ||
9-33294648-C-T | not specified | Uncertain significance (May 11, 2022) | ||
9-33294744-G-C | not specified | Uncertain significance (Jan 20, 2023) | ||
9-33295217-A-G | not specified | Uncertain significance (Nov 07, 2022) | ||
9-33295290-A-G | not specified | Uncertain significance (Aug 04, 2023) | ||
9-33295318-G-C | not specified | Uncertain significance (Jan 03, 2024) | ||
9-33295346-C-T | not specified | Uncertain significance (May 21, 2024) | ||
9-33295356-A-T | not specified | Uncertain significance (Apr 15, 2024) | ||
9-33295400-G-A | not specified | Uncertain significance (Jan 03, 2024) | ||
9-33295412-G-T | not specified | Uncertain significance (Jan 04, 2024) | ||
9-33301387-A-G | not specified | Uncertain significance (Oct 26, 2022) | ||
9-33303236-C-T | not specified | Uncertain significance (May 03, 2023) | ||
9-33307260-A-G | not specified | Likely benign (Jun 29, 2023) | ||
9-33307264-A-T | not specified | Uncertain significance (May 05, 2023) |
GnomAD
Source:
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:
- 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
- Phenotype
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