PRR5L

proline rich 5 like

Basic information

Region (hg38): 11:36296287-36465204

Links

ENSG00000135362 ∙ NCBI:79899 ∙ OMIM:611728 ∙ HGNC:25878 ∙ Uniprot:Q6MZQ0 ∙ 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 PRR5L gene.

• Inborn genetic diseases (15 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRR5L 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					3	3
missense			15		2	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	15	0	5

Variants in PRR5L

This is a list of pathogenic ClinVar variants found in the PRR5L region.

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

Position	Type	Phenotype	Significance	ClinVar
11-36401129-G-A			Benign (Dec 20, 2018)
11-36401137-G-A		not specified	Uncertain significance (Oct 14, 2023)
11-36401166-G-T		not specified	Uncertain significance (Feb 13, 2024)
11-36401243-C-A		not specified	Uncertain significance (Dec 16, 2021)
11-36401245-C-T		not specified	Uncertain significance (Mar 20, 2023)
11-36403350-G-A		not specified	Uncertain significance (Oct 20, 2023)
11-36403367-C-T			Benign (Jul 23, 2018)
11-36431865-G-A		not specified	Uncertain significance (Dec 15, 2023)
11-36437394-G-T		not specified	Uncertain significance (Jun 24, 2022)
11-36437447-A-G			Benign (Apr 19, 2019)
11-36446363-G-A		not specified	Uncertain significance (Dec 09, 2023)
11-36451290-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-36451302-G-C		not specified	Uncertain significance (Feb 27, 2023)
11-36451324-C-T		not specified	Uncertain significance (Jul 05, 2023)
11-36462348-G-A		not specified	Uncertain significance (Aug 08, 2023)
11-36462352-C-T		not specified	Likely benign (Feb 05, 2024)
11-36462395-C-T		not specified	Uncertain significance (Mar 31, 2023)
11-36462413-C-T		not specified	Uncertain significance (Dec 28, 2023)
11-36462518-T-G		not specified	Uncertain significance (Sep 22, 2023)
11-36462520-G-A			Benign (Dec 20, 2018)
11-36462565-G-T			Benign (Dec 20, 2018)
11-36462567-G-T		not specified	Uncertain significance (Dec 13, 2023)
11-36462576-C-A		not specified	Uncertain significance (Nov 08, 2022)
11-36462626-C-A		not specified	Uncertain significance (May 31, 2023)
11-36462629-C-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRR5L	protein_coding	protein_coding	ENST00000378867	8	168917

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0655	0.932	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	172	224	0.768	0.0000140	2366
Missense in Polyphen		60	95.952	0.62531		1056
Synonymous	0.161	92	94.0	0.979	0.00000584	763
Loss of Function	2.62	5	16.5	0.303	8.73e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000987	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with the mTORC2 complex that regulates cellular processes including survival and organization of the cytoskeleton (PubMed:17461779). Regulates the activity of the mTORC2 complex in a substrate-specific manner preventing for instance the specific phosphorylation of PKCs and thereby controlling cell migration (PubMed:22609986). Plays a role in the stimulation of ZFP36-mediated mRNA decay of several ZFP36- associated mRNAs, such as TNF-alpha and GM-CSF, in response to stress (PubMed:21964062). Required for ZFP36 localization to cytoplasmic stress granule (SG) and P-body (PB) in response to stress (PubMed:21964062). {ECO:0000269|PubMed:17461779, ECO:0000269|PubMed:21964062, ECO:0000269|PubMed:22609986}.
• Pathway: Target Of Rapamycin (TOR) Signaling (Consensus)

Intolerance Scores

• loftool: 0.240
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.07

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.590
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.943

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prr5l

Gene ontology

• Biological process: negative regulation of protein phosphorylation;positive regulation of protein phosphorylation;negative regulation of signal transduction;regulation of fibroblast migration;positive regulation of phosphatidylinositol 3-kinase signaling;cellular response to oxidative stress;TORC2 signaling;positive regulation of mRNA catabolic process;positive regulation of intracellular protein transport
• Cellular component: TORC2 complex
• Molecular function: protein binding;ubiquitin protein ligase binding