SRPRB

SRP receptor subunit beta

Basic information

Region (hg38): 3:133784023-133825772

Links

ENSG00000144867 ∙ NCBI:58477 ∙ OMIM:616883 ∙ HGNC:24085 ∙ Uniprot:Q9Y5M8 ∙ 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 SRPRB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRPRB 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	1

Variants in SRPRB

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

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

Position	Type	Phenotype	Significance	ClinVar
3-133805895-G-T		not specified	Uncertain significance (Sep 07, 2022)
3-133805898-G-T		not specified	Uncertain significance (Jan 08, 2024)
3-133805967-T-C		not specified	Uncertain significance (Jul 12, 2022)
3-133806614-T-C		not specified	Uncertain significance (Feb 06, 2023)
3-133806627-G-A		not specified	Uncertain significance (Oct 06, 2022)
3-133806638-A-G		not specified	Uncertain significance (Jan 18, 2022)
3-133806671-T-G		not specified	Uncertain significance (Apr 23, 2024)
3-133807769-C-A		not specified	Uncertain significance (Apr 13, 2022)
3-133807795-G-A		not specified	Uncertain significance (Jan 30, 2024)
3-133807800-G-A		not specified	Uncertain significance (May 15, 2024)
3-133807811-C-T			Benign (Dec 31, 2019)
3-133811177-G-C		not specified	Uncertain significance (Nov 17, 2022)
3-133811190-C-G		not specified	Uncertain significance (Oct 26, 2022)
3-133815628-G-A		not specified	Uncertain significance (Jun 17, 2022)
3-133815657-T-C		not specified	Uncertain significance (Mar 21, 2024)
3-133815670-T-C		not specified	Uncertain significance (Nov 17, 2022)
3-133816930-A-C			Likely benign (May 01, 2024)
3-133819567-T-C		not specified	Uncertain significance (Aug 31, 2023)
3-133819653-T-C		not specified	Uncertain significance (Aug 08, 2023)
3-133819687-G-A		not specified	Uncertain significance (Jan 03, 2024)
3-133819713-G-A		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRPRB	protein_coding	protein_coding	ENST00000466490	7	41740

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00583	0.974	125722	1	25	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00570	146	146	1.00	0.00000724	1735
Missense in Polyphen		37	45.253	0.81762		566
Synonymous	-0.00784	61	60.9	1.00	0.00000303	554
Loss of Function	2.04	6	14.3	0.419	7.91e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000117	0.000117
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.0000544	0.0000544
South Asian	0.000198	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the SRP (signal recognition particle) receptor. Ensures, in conjunction with the signal recognition particle, the correct targeting of the nascent secretory proteins to the endoplasmic reticulum membrane system. Has GTPase activity. May mediate the membrane association of SRPR (By similarity). {ECO:0000250}.
• Pathway: Protein export - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;XBP1(S) activates chaperone genes;SRP-dependent cotranslational protein targeting to membrane;Translation;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.711
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• pHI: 0.152
• hipred: N
• hipred_score: 0.333
• ghis: 0.531

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.842

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Srprb

Gene ontology

• Biological process: IRE1-mediated unfolded protein response
• Cellular component: cytoplasm;endoplasmic reticulum membrane;cytoplasmic microtubule;membrane;integral component of membrane
• Molecular function: GTP binding