RSBN1

round spermatid basic protein 1

Basic information

Region (hg38): 1:113761832-113812476

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.

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. These statistics are base on transcript: . Only rare variants are included in the table.

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 clinvar	1
missense			49 clinvar			49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	49	0	1

Loading clinvar variants...

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