RLIG1

RNA 5'-phosphate and 3'-OH ligase 1

Basic information

Region (hg38): 12:88033846-88050160

Previous symbols: [ "C12orf29" ]

Links

ENSG00000133641 ∙ NCBI:91298 ∙ ∙ HGNC:25322 ∙ Uniprot:Q8N999 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RLIG1 gene.

• Bardet-Biedl syndrome 14 (4 variants)
• Familial aplasia of the vermis;Nephronophthisis;Meckel-Gruber syndrome (3 variants)
• Leber congenital amaurosis (3 variants)
• Familial aplasia of the vermis;Meckel-Gruber syndrome;Nephronophthisis (2 variants)
• Joubert syndrome 5 (2 variants)
• Meckel-Gruber syndrome;Familial aplasia of the vermis;Nephronophthisis (2 variants)
• CEP290-related disorder (2 variants)
• Bardet-Biedl syndrome 14;Senior-Loken syndrome 6;Leber congenital amaurosis 10;Meckel syndrome, type 4;Joubert syndrome 5 (1 variants)
• not provided (1 variants)
• Inborn genetic diseases (1 variants)
• Senior-Loken syndrome 6;Bardet-Biedl syndrome 14;Joubert syndrome 5;Leber congenital amaurosis 10;Meckel syndrome, type 4 (1 variants)
• Leber congenital amaurosis 10 (1 variants)
• Retinal dystrophy (1 variants)
• Joubert syndrome 5;Leber congenital amaurosis 10;Meckel syndrome, type 4;Bardet-Biedl syndrome 14;Senior-Loken syndrome 6 (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	9	20	45	33		107
Total	9	20	45	33	0

Highest pathogenic variant AF is 0.0000198

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		Bardet-Biedl syndrome 14 • Leber congenital amaurosis 10 • Joubert syndrome 5 • Senior-Loken syndrome 6 • Meckel syndrome, type 4	Uncertain significance (Jan 12, 2018)
12-88049033-A-G		Meckel syndrome, type 4 • Bardet-Biedl syndrome 14 • Joubert syndrome 5 • 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 • Joubert syndrome • 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 • Joubert syndrome • Leber congenital amaurosis	Benign/Likely benign (May 10, 2018)
12-88049187-G-A		Meckel-Gruber syndrome;Nephronophthisis;Joubert syndrome	Likely benign (Mar 04, 2022)
12-88049194-G-C		Joubert syndrome;Nephronophthisis;Meckel-Gruber syndrome • CEP290-related disorder	Uncertain significance (Jun 29, 2022)
12-88049195-G-C		Joubert syndrome 5;Bardet-Biedl syndrome 14;Meckel syndrome, type 4;Senior-Loken syndrome 6;Leber congenital amaurosis 10	Uncertain significance (Apr 22, 2024)
12-88049199-A-G		Joubert syndrome;Meckel-Gruber syndrome;Nephronophthisis	Likely benign (Sep 27, 2022)
12-88049201-T-G		CEP290-related disorder	Uncertain significance (Aug 14, 2024)
12-88049202-A-G		Nephronophthisis;Meckel-Gruber syndrome;Joubert syndrome	Likely benign (Sep 26, 2023)
12-88049208-A-G		Joubert syndrome;Meckel-Gruber syndrome;Nephronophthisis	Likely benign (Aug 20, 2022)
12-88049208-A-T		Joubert syndrome;Meckel-Gruber syndrome;Nephronophthisis • CEP290-related disorder • Leber congenital amaurosis 10;Joubert syndrome 5;Meckel syndrome, type 4;Bardet-Biedl syndrome 14;Senior-Loken syndrome 6	Uncertain significance (Jan 09, 2024)
12-88049210-TTTC-T		Joubert syndrome;Meckel-Gruber syndrome;Nephronophthisis • Leber congenital amaurosis	Uncertain significance (Aug 31, 2021)
12-88049211-TTC-T		Joubert syndrome;Meckel-Gruber syndrome;Nephronophthisis • CEP290-related disorder	Uncertain significance (Feb 24, 2022)
12-88049213-C-T		Joubert syndrome;Nephronophthisis;Meckel-Gruber syndrome • Retinal dystrophy • Inborn genetic diseases • Joubert syndrome 5;Meckel syndrome, type 4;Senior-Loken syndrome 6;Bardet-Biedl syndrome 14;Leber congenital amaurosis 10	Uncertain significance (Apr 04, 2024)
12-88049216-C-T		Joubert syndrome 5;Bardet-Biedl syndrome 14;Meckel syndrome, type 4;Senior-Loken syndrome 6;Leber congenital amaurosis 10	Uncertain significance (Apr 12, 2024)
12-88049227-A-G		Joubert syndrome;Meckel-Gruber syndrome;Nephronophthisis • Leber congenital amaurosis • CEP290-related disorder	Uncertain significance (Sep 13, 2022)
12-88049227-A-T		Joubert syndrome;Meckel-Gruber syndrome;Nephronophthisis • Inborn genetic diseases • Meckel syndrome, type 4;Leber congenital amaurosis 10;Senior-Loken syndrome 6;Bardet-Biedl syndrome 14;Joubert syndrome 5	Uncertain significance (Mar 13, 2024)
12-88049226-A-AAACT		Joubert syndrome;Meckel-Gruber syndrome;Nephronophthisis	Uncertain significance (Dec 02, 2024)
12-88049228-ACT-A		not specified • Bardet-Biedl syndrome 14 • Joubert syndrome 5 • Nephronophthisis;Meckel-Gruber syndrome;Joubert syndrome • Retinal dystrophy • Senior-Loken syndrome 6;Meckel syndrome, type 4;Leber congenital amaurosis 10;Bardet-Biedl syndrome 14;Joubert syndrome 5 • CEP290-related disorder	Conflicting classifications of pathogenicity (Jan 06, 2025)
12-88049228-A-ACTC		Nephronophthisis;Meckel-Gruber syndrome;Joubert syndrome	Uncertain significance (Aug 23, 2023)
12-88049230-T-G		CEP290-related disorder • Inborn genetic diseases	Uncertain significance (Jan 08, 2025)
12-88049231-C-CTG		Joubert syndrome;Meckel-Gruber syndrome;Nephronophthisis • Leber congenital amaurosis • CEP290-related disorder • Leber congenital amaurosis 10;Senior-Loken syndrome 6;Joubert syndrome 5;Meckel syndrome, type 4;Bardet-Biedl syndrome 14	Uncertain significance (Sep 30, 2024)
12-88049235-A-G		Joubert syndrome;Nephronophthisis;Meckel-Gruber syndrome	Likely benign (Dec 24, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

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 Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: 4930430F08Rik

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation