RTBDN

retbindin

Basic information

Region (hg38): 19:12825478-12835428

Links

ENSG00000132026 ∙ NCBI:83546 ∙ OMIM:609553 ∙ HGNC:30310 ∙ Uniprot:Q9BSG5 ∙ 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 RTBDN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTBDN 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	1
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	1

Variants in RTBDN

This is a list of pathogenic ClinVar variants found in the RTBDN region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-12825767-C-G		not specified	Uncertain significance (Jan 06, 2023)
19-12825830-A-C		not specified	Uncertain significance (Apr 07, 2022)
19-12825887-G-A		not specified	Uncertain significance (Dec 28, 2023)
19-12825921-C-G		not specified	Uncertain significance (Dec 18, 2023)
19-12826813-T-C		not specified	Uncertain significance (Nov 06, 2023)
19-12826822-G-A		not specified	Uncertain significance (Dec 15, 2022)
19-12826836-G-A		not specified	Uncertain significance (Jun 02, 2024)
19-12826836-G-T		not specified	Uncertain significance (Jan 24, 2024)
19-12826851-T-C		not specified	Uncertain significance (Sep 06, 2022)
19-12826863-T-C		not specified	Uncertain significance (Jul 21, 2021)
19-12828669-A-G		not specified	Uncertain significance (Jan 16, 2024)
19-12828693-T-C		not specified	Uncertain significance (Oct 14, 2021)
19-12828697-G-A		not specified	Uncertain significance (Oct 29, 2021)
19-12828712-G-A		not specified	Uncertain significance (Jun 30, 2023)
19-12828719-G-C		not specified	Uncertain significance (Apr 19, 2024)
19-12828735-G-A		not specified	Uncertain significance (Apr 12, 2022)
19-12828751-C-G		not specified	Uncertain significance (May 16, 2023)
19-12828932-A-C		not specified	Uncertain significance (Jan 30, 2024)
19-12829825-T-A		not specified	Uncertain significance (Jan 03, 2022)
19-12829879-A-T		not specified	Uncertain significance (May 03, 2023)
19-12829885-C-T		not specified	Likely benign (Nov 09, 2022)
19-12829886-G-A		not specified	Uncertain significance (May 14, 2024)
19-12829923-G-A			Benign (Jul 13, 2018)
19-12829968-C-A		not specified	Uncertain significance (Aug 17, 2022)
19-12834789-A-G		not specified	Uncertain significance (Dec 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTBDN	protein_coding	protein_coding	ENST00000322912	7	9951

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.02e-10	0.0460	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.204	165	158	1.05	0.00000798	1643
Missense in Polyphen		33	38.598	0.85497		458
Synonymous	0.0301	64	64.3	0.995	0.00000333	561
Loss of Function	-0.285	14	12.9	1.09	6.35e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000416	0.000416
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000658	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Riboflavin-binding protein which might have a role in retinal flavin transport. {ECO:0000250|UniProtKB:Q8QZY4}.

Recessive Scores

• pRec: 0.0964

Intolerance Scores

• loftool: 0.895
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.220
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.131

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rtbdn
• Phenotype: vision/eye phenotype; hematopoietic system phenotype; pigmentation phenotype

Gene ontology

• Biological process: riboflavin transport
• Cellular component: anchored component of external side of plasma membrane;interphotoreceptor matrix
• Molecular function: riboflavin transmembrane transporter activity;signaling receptor activity;riboflavin binding