RSBN1

round spermatid basic protein 1

Basic information

Region (hg38): 1:113761831-113812476

Links

ENSG00000081019 ∙ NCBI:54665 ∙ OMIM:615858 ∙ HGNC:25642 ∙ Uniprot:Q5VWQ0 ∙ 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 RSBN1 gene.

• Inborn genetic diseases (23 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RSBN1 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	1

Variants in RSBN1

This is a list of pathogenic ClinVar variants found in the RSBN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-113765994-T-C		not specified	Uncertain significance (Dec 21, 2022)
1-113766075-G-C		not specified	Uncertain significance (May 23, 2023)
1-113766136-C-G		not specified	Uncertain significance (Dec 01, 2022)
1-113766248-G-C		not specified	Uncertain significance (Apr 20, 2023)
1-113766284-T-C		not specified	Uncertain significance (May 18, 2023)
1-113766317-G-A		not specified	Uncertain significance (Sep 14, 2022)
1-113768303-T-C		not specified	Uncertain significance (Jun 24, 2022)
1-113768335-G-A			Benign (Feb 01, 2018)
1-113777790-A-T		not specified	Uncertain significance (Feb 15, 2023)
1-113797394-T-C		not specified	Uncertain significance (Aug 13, 2021)
1-113797581-C-T		not specified	Uncertain significance (Dec 14, 2022)
1-113797674-A-G		not specified	Uncertain significance (Dec 06, 2023)
1-113797718-T-C		not specified	Uncertain significance (Apr 07, 2022)
1-113797825-A-T		not specified	Uncertain significance (Jan 24, 2024)
1-113797839-T-C		not specified	Uncertain significance (Dec 01, 2022)
1-113797899-C-T		not specified	Uncertain significance (Aug 09, 2021)
1-113797909-T-A		not specified	Uncertain significance (Oct 26, 2022)
1-113797929-G-A		not specified	Uncertain significance (Aug 11, 2022)
1-113797944-T-C		not specified	Uncertain significance (Feb 05, 2024)
1-113811775-T-G		not specified	Uncertain significance (Aug 09, 2021)
1-113811799-C-A		not specified	Uncertain significance (May 27, 2022)
1-113811855-C-G		not specified	Uncertain significance (Nov 13, 2023)
1-113811861-C-A		not specified	Uncertain significance (Feb 21, 2024)
1-113811925-G-A		not specified	Uncertain significance (Feb 23, 2023)
1-113811929-G-C		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RSBN1	protein_coding	protein_coding	ENST00000261441	7	50645

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0991	0.901	125582	2	164	125748	0.000660

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	315	440	0.717	0.0000222	5223
Missense in Polyphen		71	157.2	0.45165		1885
Synonymous	0.210	159	162	0.979	0.00000802	1590
Loss of Function	4.11	9	35.3	0.255	0.00000224	369

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00272	0.00261
Ashkenazi Jewish	0.00	0.00
East Asian	0.000610	0.000598
Finnish	0.000200	0.000139
European (Non-Finnish)	0.000603	0.000554
Middle Eastern	0.000610	0.000598
South Asian	0.000460	0.000457
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone demethylase that specifically demethylates dimethylated 'Lys-20' of histone H4 (H4K20me2), thereby modulating chromosome architecture. {ECO:0000250|UniProtKB:Q80T69}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.177
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.18

Haploinsufficiency Scores

• pHI: 0.583
• hipred: Y
• hipred_score: 0.575
• ghis: 0.629

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.909

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rsbn1
• 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); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: chromatin organization;oxidation-reduction process
• Cellular component: nucleus
• Molecular function: metal ion binding;dioxygenase activity