RFX7
Basic information
Region (hg38): 15:56087279-56245082
Previous symbols: [ "RFXDC2" ]
Links
Phenotypes
GenCC
Source:
- intellectual developmental disorder, autosomal dominant 71, with behavioral abnormalities (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Intellectual developmental disorder, autosomal dominant 71, with behavioral abnormalities | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic | 33658631; 36334883 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (61 variants)
- not provided (36 variants)
- Intellectual developmental disorder, autosomal dominant 71, with behavioral abnormalities (5 variants)
- RFX7-related condition (4 variants)
- not specified (2 variants)
- Neurodevelopmental disorder (1 variants)
- See cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFX7 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 | 5 | |||||
missense | 62 | 16 | 82 | |||
nonsense | 6 | |||||
start loss | 0 | |||||
frameshift | 6 | |||||
inframe indel | 3 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 3 | |||||
Total | 1 | 3 | 73 | 21 | 7 |
Variants in RFX7
This is a list of pathogenic ClinVar variants found in the RFX7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
15-56093369-A-C | RFX7-related disorder | Uncertain significance (Apr 20, 2023) | ||
15-56093460-A-C | RFX7-related disorder | Uncertain significance (Jul 28, 2023) | ||
15-56093544-T-C | Inborn genetic diseases | Likely benign (Dec 08, 2023) | ||
15-56093577-A-G | Inborn genetic diseases | Likely benign (Nov 13, 2023) | ||
15-56093639-C-G | Uncertain significance (Jul 05, 2022) | |||
15-56093661-C-A | Inborn genetic diseases | Uncertain significance (Aug 30, 2021) | ||
15-56093661-C-G | Inborn genetic diseases | Uncertain significance (Aug 17, 2022) | ||
15-56093688-T-C | Inborn genetic diseases | Likely benign (Mar 06, 2023) | ||
15-56093712-A-G | Inborn genetic diseases | Uncertain significance (Jul 11, 2023) | ||
15-56093754-T-G | Inborn genetic diseases | Uncertain significance (Jul 25, 2023) | ||
15-56093757-C-T | Inborn genetic diseases | Likely benign (Aug 04, 2021) | ||
15-56093786-TG-T | Uncertain significance (Jun 20, 2019) | |||
15-56093877-G-A | Uncertain significance (Mar 24, 2023) | |||
15-56093940-T-C | Inborn genetic diseases | Uncertain significance (Jul 25, 2023) | ||
15-56093944-CATT-C | Intellectual developmental disorder, autosomal dominant 71, with behavioral abnormalities | Uncertain significance (Mar 29, 2024) | ||
15-56093976-T-C | Inborn genetic diseases | Likely benign (Nov 13, 2023) | ||
15-56093977-T-C | Inborn genetic diseases | Uncertain significance (Jan 11, 2023) | ||
15-56093997-G-A | Inborn genetic diseases | Uncertain significance (Jun 30, 2022) | ||
15-56094159-C-T | Inborn genetic diseases | Uncertain significance (Nov 08, 2022) | ||
15-56094234-C-T | Inborn genetic diseases | Likely benign (Dec 01, 2022) | ||
15-56094235-G-A | Inborn genetic diseases | Likely benign (Jul 14, 2022) | ||
15-56094316-T-A | Benign (Apr 09, 2018) | |||
15-56094331-T-C | Inborn genetic diseases | Uncertain significance (Nov 19, 2022) | ||
15-56094349-C-G | Inborn genetic diseases | Uncertain significance (Jan 22, 2024) | ||
15-56094369-C-T | Inborn genetic diseases | Uncertain significance (Feb 01, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RFX7 | protein_coding | protein_coding | ENST00000423270 | 9 | 156006 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 8.88e-7 | 124622 | 0 | 7 | 124629 | 0.0000281 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.60 | 637 | 761 | 0.837 | 0.0000388 | 9587 |
Missense in Polyphen | 201 | 328.1 | 0.61262 | 4112 | ||
Synonymous | -0.252 | 280 | 275 | 1.02 | 0.0000143 | 2908 |
Loss of Function | 6.13 | 2 | 47.6 | 0.0420 | 0.00000234 | 601 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000189 | 0.000167 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000355 | 0.0000354 |
Middle Eastern | 0.000189 | 0.000167 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
Recessive Scores
- pRec
- 0.103
Haploinsufficiency Scores
- pHI
- 0.765
- hipred
- Y
- hipred_score
- 0.644
- ghis
- 0.648
Essentials
- essential_gene_CRISPR
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.488
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rfx7
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype;
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II
- Cellular component
- nucleus
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity