RFX2

regulatory factor X2, the group of Regulatory factor X family

Basic information

Region (hg38): 19:5993164-6199572

Links

ENSG00000087903NCBI:5990OMIM:142765HGNC:9983Uniprot:P48378AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • cerebral palsy (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RFX2 gene.

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
1
clinvar
1
clinvar
2
missense
47
clinvar
5
clinvar
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)2463753
19-5994869-C-T not specified Uncertain significance (Feb 08, 2023)2460028
19-5994902-C-T not specified Likely benign (May 26, 2022)2261960
19-5994917-G-A not specified Uncertain significance (Mar 29, 2022)2366896
19-5994929-C-T not specified Uncertain significance (May 27, 2022)2397203
19-5994936-C-T not specified Uncertain significance (Mar 20, 2023)2525191
19-5995603-T-G not specified Uncertain significance (Apr 24, 2024)3313929
19-5995607-C-T not specified Uncertain significance (Oct 12, 2021)2254457
19-5995631-C-T not specified Uncertain significance (Apr 04, 2024)3313921
19-5997105-G-A Likely benign (Nov 01, 2022)2649129
19-6001866-G-A not specified Uncertain significance (Jun 16, 2024)3313923
19-6001896-G-A not specified Uncertain significance (Nov 15, 2021)2261688
19-6001905-C-A not specified Uncertain significance (May 31, 2023)2554589
19-6001920-G-A not specified Uncertain significance (Jan 16, 2024)3153466
19-6001977-C-T not specified Uncertain significance (Jan 24, 2023)2471421
19-6002753-C-T not specified Uncertain significance (Jan 29, 2024)3153465
19-6002797-C-T not specified Uncertain significance (Aug 14, 2023)2593809
19-6002836-C-G not specified Uncertain significance (Apr 12, 2022)2283302
19-6002861-C-T not specified Uncertain significance (Apr 06, 2024)3313927
19-6004280-A-G Tooth agenesis • not specified Uncertain significance (Aug 12, 2021)1285613
19-6004295-G-A not specified Uncertain significance (Nov 01, 2021)2258581
19-6007020-G-A not specified Uncertain significance (Aug 03, 2022)2412277
19-6007106-G-C not specified Uncertain significance (Jun 06, 2023)2558083
19-6007153-C-T not specified Uncertain significance (Apr 23, 2024)3313928
19-6007712-C-T not specified Uncertain significance (Jul 19, 2022)2358130

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RFX2protein_codingprotein_codingENST00000303657 17206409
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000302125401061254070.0000239
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.663084700.6550.00003194669
Missense in Polyphen83158.870.522441543
Synonymous1.061982180.9080.00001751432
Loss of Function5.13336.50.08230.00000165392

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001110.000111
Ashkenazi Jewish0.0001070.0000999
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001800.0000176
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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