PRR15L

proline rich 15 like

Basic information

Region (hg38): 17:47951967-47957883

Previous symbols: [ "ATAD4" ]

Links

ENSG00000167183 ∙ NCBI:79170 ∙ ∙ HGNC:28149 ∙ Uniprot:Q9BU68 ∙ 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 PRR15L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRR15L 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						0
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in PRR15L

This is a list of pathogenic ClinVar variants found in the PRR15L region.

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

Position	Type	Phenotype	Significance	ClinVar
17-47952936-C-T		not specified	Likely benign (Oct 29, 2021)
17-47952937-G-A		not specified	Uncertain significance (Jan 24, 2025)
17-47952940-C-T		not specified	Uncertain significance (May 17, 2023)
17-47952950-A-C		not specified	Uncertain significance (Apr 19, 2023)
17-47952981-G-A		not specified	Uncertain significance (Jun 06, 2023)
17-47953005-T-C		not specified	Uncertain significance (Aug 11, 2022)
17-47953011-C-T		not specified	Uncertain significance (Oct 12, 2022)
17-47953033-C-T		not specified	Uncertain significance (Aug 01, 2022)
17-47953035-T-C		not specified	Uncertain significance (Aug 08, 2023)
17-47953052-C-G		not specified	Uncertain significance (Nov 10, 2024)
17-47953088-G-C		not specified	Uncertain significance (Jan 14, 2025)
17-47953092-T-C		not specified	Uncertain significance (Feb 10, 2022)
17-47953098-C-T		not specified	Uncertain significance (Jul 08, 2021)
17-47953116-G-A		not specified	Uncertain significance (Apr 05, 2023)
17-47953140-T-G		not specified	Uncertain significance (Aug 19, 2024)
17-47953230-G-T		not specified	Uncertain significance (May 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRR15L	protein_coding	protein_coding	ENST00000300557	1	5912

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.510	0.427	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.106	65	62.6	1.04	0.00000390	666
Missense in Polyphen		17	21.244	0.80021		248
Synonymous	0.189	25	26.2	0.953	0.00000173	204
Loss of Function	1.32	0	2.03	0.00	8.44e-8	32

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)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.281
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.0899
• hipred: N
• hipred_score: 0.213
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prr15l