RFX2
Basic information
Region (hg38): 19:5993164-6199572
Links
Phenotypes
GenCC
Source:
- cerebral palsy (Limited), mode of inheritance: AD
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 RFX2 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 | 2 | |||||
missense | 47 | 52 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 47 | 6 | 1 |
Variants in RFX2
This is a list of pathogenic ClinVar variants found in the RFX2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
19-5994855-G-A | not specified | Uncertain significance (Feb 16, 2023) | ||
19-5994869-C-T | not specified | Uncertain significance (Feb 08, 2023) | ||
19-5994902-C-T | not specified | Likely benign (May 26, 2022) | ||
19-5994917-G-A | not specified | Uncertain significance (Mar 29, 2022) | ||
19-5994929-C-T | not specified | Uncertain significance (May 27, 2022) | ||
19-5994936-C-T | not specified | Uncertain significance (Mar 20, 2023) | ||
19-5995603-T-G | not specified | Uncertain significance (Apr 24, 2024) | ||
19-5995607-C-T | not specified | Uncertain significance (Oct 12, 2021) | ||
19-5995631-C-T | not specified | Uncertain significance (Apr 04, 2024) | ||
19-5997105-G-A | Likely benign (Nov 01, 2022) | |||
19-6001866-G-A | not specified | Uncertain significance (Jun 16, 2024) | ||
19-6001896-G-A | not specified | Uncertain significance (Nov 15, 2021) | ||
19-6001905-C-A | not specified | Uncertain significance (May 31, 2023) | ||
19-6001920-G-A | not specified | Uncertain significance (Jan 16, 2024) | ||
19-6001977-C-T | not specified | Uncertain significance (Jan 24, 2023) | ||
19-6002753-C-T | not specified | Uncertain significance (Jan 29, 2024) | ||
19-6002797-C-T | not specified | Uncertain significance (Aug 14, 2023) | ||
19-6002836-C-G | not specified | Uncertain significance (Apr 12, 2022) | ||
19-6002861-C-T | not specified | Uncertain significance (Apr 06, 2024) | ||
19-6004280-A-G | Tooth agenesis • not specified | Uncertain significance (Aug 12, 2021) | ||
19-6004295-G-A | not specified | Uncertain significance (Nov 01, 2021) | ||
19-6007020-G-A | not specified | Uncertain significance (Aug 03, 2022) | ||
19-6007106-G-C | not specified | Uncertain significance (Jun 06, 2023) | ||
19-6007153-C-T | not specified | Uncertain significance (Apr 23, 2024) | ||
19-6007712-C-T | not specified | Uncertain significance (Jul 19, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RFX2 | protein_coding | protein_coding | ENST00000303657 | 17 | 206409 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 0.000302 | 125401 | 0 | 6 | 125407 | 0.0000239 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.66 | 308 | 470 | 0.655 | 0.0000319 | 4669 |
Missense in Polyphen | 83 | 158.87 | 0.52244 | 1543 | ||
Synonymous | 1.06 | 198 | 218 | 0.908 | 0.0000175 | 1432 |
Loss of Function | 5.13 | 3 | 36.5 | 0.0823 | 0.00000165 | 392 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000111 | 0.000111 |
Ashkenazi Jewish | 0.000107 | 0.0000999 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000180 | 0.0000176 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor that acts as a key regulator of spermatogenesis. Acts by regulating expression of genes required for the haploid phase during spermiogenesis, such as genes required for cilium assembly and function (By similarity). Recognizes and binds the X-box, a regulatory motif with DNA sequence 5'-GTNRCC(0-3N)RGYAAC-3' present on promoters (PubMed:10330134). Probably activates transcription of the testis- specific histone gene HIST1H1T (By similarity). {ECO:0000250|UniProtKB:P48379, ECO:0000269|PubMed:10330134}.;
Recessive Scores
- pRec
- 0.131
Intolerance Scores
- loftool
- 0.177
- rvis_EVS
- -0.86
- rvis_percentile_EVS
- 10.89
Haploinsufficiency Scores
- pHI
- 0.804
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.507
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.907
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rfx2
- Phenotype
- reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- rfx2
- Affected structure
- liver
- Phenotype tag
- abnormal
- Phenotype quality
- symmetry
Gene ontology
- Biological process
- acrosome assembly;regulation of transcription by RNA polymerase II;spermatid development;positive regulation of transcription by RNA polymerase II;cilium assembly;cellular response to leukemia inhibitory factor
- Cellular component
- nucleus;cytoplasm
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding