RLIG1
Basic information
Region (hg38): 12:88033845-88050160
Previous symbols: [ "C12orf29" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- Bardet-Biedl syndrome 14 (2 variants)
- Nephronophthisis;Meckel-Gruber syndrome;Familial aplasia of the vermis (2 variants)
- Leber congenital amaurosis 10;Senior-Loken syndrome 6;Joubert syndrome 5;Meckel syndrome, type 4;Bardet-Biedl syndrome 14 (1 variants)
- Familial aplasia of the vermis;Nephronophthisis;Meckel-Gruber syndrome (1 variants)
- Familial aplasia of the vermis;Meckel-Gruber syndrome;Nephronophthisis (1 variants)
- Joubert syndrome 5 (1 variants)
- Leber congenital amaurosis (1 variants)
- Meckel-Gruber syndrome;Nephronophthisis;Familial aplasia of the vermis (1 variants)
- CEP290-related disorder (1 variants)
- Retinal dystrophy (1 variants)
- Nephronophthisis;Familial aplasia of the vermis;Meckel-Gruber syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RLIG1 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 | 0 | |||||
missense | 0 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 19 | 39 | 33 | 99 | ||
Total | 8 | 19 | 39 | 33 | 0 |
Highest pathogenic variant AF is 0.00000658
Variants in RLIG1
This is a list of pathogenic ClinVar variants found in the RLIG1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
12-88049016-T-C | Meckel syndrome, type 4 • Bardet-Biedl syndrome 14 • Leber congenital amaurosis 10 • Joubert syndrome 5 • Senior-Loken syndrome 6 | Uncertain significance (Jan 12, 2018) | ||
12-88049033-A-G | Joubert syndrome 5 • Meckel syndrome, type 4 • Bardet-Biedl syndrome 14 • Senior-Loken syndrome 6 • Leber congenital amaurosis 10 | Uncertain significance (Jan 12, 2018) | ||
12-88049037-TTTTA-T | Renal dysplasia and retinal aplasia • Leber congenital amaurosis • Familial aplasia of the vermis • Meckel-Gruber syndrome • Bardet-Biedl syndrome | Uncertain significance (Jun 14, 2016) | ||
12-88049140-A-T | not specified | Likely benign (-) | ||
12-88049161-GAAAC-G | not specified • Bardet-Biedl syndrome • Renal dysplasia and retinal aplasia • Meckel-Gruber syndrome • Familial aplasia of the vermis • Leber congenital amaurosis | Benign/Likely benign (May 10, 2018) | ||
12-88049187-G-A | Meckel-Gruber syndrome;Familial aplasia of the vermis;Nephronophthisis | Likely benign (Mar 04, 2022) | ||
12-88049194-G-C | Meckel-Gruber syndrome;Nephronophthisis;Familial aplasia of the vermis | Uncertain significance (Jun 29, 2022) | ||
12-88049199-A-G | Nephronophthisis;Familial aplasia of the vermis;Meckel-Gruber syndrome | Likely benign (Sep 27, 2022) | ||
12-88049202-A-G | Nephronophthisis;Meckel-Gruber syndrome;Familial aplasia of the vermis | Likely benign (Sep 26, 2023) | ||
12-88049208-A-G | Meckel-Gruber syndrome;Familial aplasia of the vermis;Nephronophthisis | Likely benign (Aug 20, 2022) | ||
12-88049208-A-T | Meckel-Gruber syndrome;Nephronophthisis;Familial aplasia of the vermis | Uncertain significance (Aug 23, 2022) | ||
12-88049210-TTTC-T | Familial aplasia of the vermis;Meckel-Gruber syndrome;Nephronophthisis • Leber congenital amaurosis | Uncertain significance (Aug 31, 2021) | ||
12-88049211-TTC-T | Meckel-Gruber syndrome;Familial aplasia of the vermis;Nephronophthisis • CEP290-related disorder | Uncertain significance (Feb 01, 2024) | ||
12-88049213-C-T | Meckel-Gruber syndrome;Nephronophthisis;Familial aplasia of the vermis • Retinal dystrophy • Inborn genetic diseases | Uncertain significance (Nov 27, 2023) | ||
12-88049227-A-G | Meckel-Gruber syndrome;Familial aplasia of the vermis;Nephronophthisis • Leber congenital amaurosis | Uncertain significance (Sep 13, 2022) | ||
12-88049227-A-T | Familial aplasia of the vermis;Meckel-Gruber syndrome;Nephronophthisis • Inborn genetic diseases | Uncertain significance (Feb 22, 2023) | ||
12-88049226-A-AAACT | Meckel-Gruber syndrome;Familial aplasia of the vermis;Nephronophthisis | Uncertain significance (Aug 12, 2022) | ||
12-88049228-ACT-A | not specified • Bardet-Biedl syndrome 14 • Joubert syndrome 5 • Familial aplasia of the vermis;Meckel-Gruber syndrome;Nephronophthisis | Conflicting classifications of pathogenicity (Jan 27, 2024) | ||
12-88049228-A-ACTC | Nephronophthisis;Meckel-Gruber syndrome;Familial aplasia of the vermis | Uncertain significance (Aug 23, 2023) | ||
12-88049231-C-CTG | Leber congenital amaurosis • Familial aplasia of the vermis;Meckel-Gruber syndrome;Nephronophthisis • CEP290-related disorder | Uncertain significance (Dec 20, 2023) | ||
12-88049237-AAGC-A | Familial aplasia of the vermis;Meckel-Gruber syndrome;Nephronophthisis • Leber congenital amaurosis | Uncertain significance (Aug 31, 2022) | ||
12-88049238-A-C | Familial aplasia of the vermis;Nephronophthisis;Meckel-Gruber syndrome | Likely benign (Jul 25, 2022) | ||
12-88049244-A-T | Familial aplasia of the vermis;Nephronophthisis;Meckel-Gruber syndrome | Likely benign (Oct 16, 2023) | ||
12-88049249-G-A | Senior-Loken syndrome 6 • Bardet-Biedl syndrome 14 • Leber congenital amaurosis 10 • Joubert syndrome 5 • Meckel syndrome, type 4 • Meckel-Gruber syndrome;Nephronophthisis;Familial aplasia of the vermis | Uncertain significance (Jul 19, 2022) | ||
12-88049250-G-A | Meckel-Gruber syndrome;Nephronophthisis;Familial aplasia of the vermis | Likely benign (Oct 08, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RLIG1 | protein_coding | protein_coding | ENST00000356891 | 7 | 16315 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.11e-8 | 0.263 | 125653 | 0 | 95 | 125748 | 0.000378 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.820 | 131 | 160 | 0.818 | 0.00000724 | 2156 |
Missense in Polyphen | 31 | 46.126 | 0.67207 | 634 | ||
Synonymous | -0.0960 | 55 | 54.1 | 1.02 | 0.00000255 | 558 |
Loss of Function | 0.520 | 13 | 15.2 | 0.856 | 6.94e-7 | 211 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000587 | 0.000575 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000451 | 0.000435 |
Finnish | 0.0000466 | 0.0000462 |
European (Non-Finnish) | 0.000480 | 0.000457 |
Middle Eastern | 0.000451 | 0.000435 |
South Asian | 0.000656 | 0.000621 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
Recessive Scores
- pRec
- 0.0780
Intolerance Scores
- loftool
- 0.808
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.49
Haploinsufficiency Scores
- pHI
- 0.251
- hipred
- N
- hipred_score
- 0.251
- ghis
- 0.588
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- 4930430F08Rik
- Phenotype
Gene ontology
- Biological process
- hematopoietic progenitor cell differentiation
- Cellular component
- Molecular function