SRP19

signal recognition particle 19, the group of Signal recognition particle

Basic information

Region (hg38): 5:112861188-112898371

Links

ENSG00000153037 ∙ NCBI:6728 ∙ OMIM:182175 ∙ HGNC:11300 ∙ Uniprot:P09132 ∙ 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 SRP19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRP19 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in SRP19

This is a list of pathogenic ClinVar variants found in the SRP19 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-112861381-C-A		not specified	Uncertain significance (May 26, 2024)
5-112861384-G-A		not specified	Uncertain significance (Jul 29, 2022)
5-112861387-C-G		not specified	Uncertain significance (Jan 18, 2023)
5-112861395-C-T		not specified	Uncertain significance (Apr 26, 2023)
5-112861407-G-A		not specified	Uncertain significance (Dec 02, 2022)
5-112862510-T-C		not specified	Uncertain significance (Mar 27, 2023)
5-112864519-A-C		not specified	Likely benign (Oct 27, 2023)
5-112864533-G-A		Shwachman-Diamond syndrome 1;Severe congenital neutropenia	Pathogenic (Jan 06, 2020)
5-112867428-C-T		not specified	Uncertain significance (Feb 06, 2024)
5-112867437-T-C		not specified	Uncertain significance (May 20, 2024)
5-112867452-C-T		not specified	Uncertain significance (May 30, 2023)
5-112867501-G-T		not specified	Uncertain significance (Sep 20, 2023)
5-112887090-C-T			Benign (Aug 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRP19	protein_coding	protein_coding	ENST00000505459	5	8567

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00690	0.925	125735	0	6	125741	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.257	73	79.5	0.919	0.00000403	929
Missense in Polyphen		11	17.005	0.64688		206
Synonymous	-0.626	30	25.9	1.16	0.00000122	261
Loss of Function	1.57	5	10.5	0.476	6.30e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Signal-recognition-particle assembly, binds directly to 7S RNA and mediates binding of the 54 kDa subunit of the SRP.
• Pathway: Protein export - Homo sapiens (human);SRP-dependent cotranslational protein targeting to membrane;Translation;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.157

Intolerance Scores

• loftool: 0.572
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.0943
• hipred: Y
• hipred_score: 0.617
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Srp19

Gene ontology

• Biological process: cotranslational protein targeting to membrane;SRP-dependent cotranslational protein targeting to membrane;SRP-dependent cotranslational protein targeting to membrane, translocation;SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition;response to drug
• Cellular component: nucleolus;signal recognition particle, endoplasmic reticulum targeting;cytosol;signal recognition particle
• Molecular function: RNA binding;protein binding;7S RNA binding;ribosome binding