PARL

presenilin associated rhomboid like, the group of Rhomboid family

Basic information

Region (hg38): 3:183829271-183884933

Previous symbols: [ "PSARL" ]

Links

ENSG00000175193 ∙ NCBI:55486 ∙ OMIM:607858 ∙ HGNC:18253 ∙ Uniprot:Q9H300 ∙ 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 PARL gene.

Variants pathogenicity by type

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

Variants in PARL

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

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

Position	Type	Phenotype	Significance	ClinVar
3-183829707-C-A		not specified	Uncertain significance (Jul 12, 2022)
3-183833534-A-C		not specified	Uncertain significance (Feb 27, 2024)
3-183833731-G-A		not specified	Uncertain significance (Dec 06, 2021)
3-183833762-T-C		not specified	Uncertain significance (Mar 08, 2024)
3-183833767-A-C		not specified	Uncertain significance (Feb 27, 2023)
3-183840578-G-A		not specified	Uncertain significance (Jun 17, 2024)
3-183840585-T-C			Uncertain significance (Aug 01, 2024)
3-183844245-G-A		not specified	Uncertain significance (Feb 10, 2022)
3-183844270-G-A		not specified	Uncertain significance (Jun 28, 2022)
3-183857982-G-A		Leprosy, susceptibility to, 1	Uncertain risk allele (Jun 10, 2022)
3-183862779-A-G		not specified	Uncertain significance (Feb 06, 2024)
3-183866637-G-T		not specified	Uncertain significance (May 30, 2024)
3-183866755-C-T		not specified	Uncertain significance (May 20, 2024)
3-183867896-C-T		not specified	Uncertain significance (Sep 20, 2023)
3-183867905-G-A		not specified	Uncertain significance (Mar 18, 2024)
3-183867911-G-A		not specified	Uncertain significance (Aug 04, 2021)
3-183867956-C-T			Uncertain significance (Nov 01, 2011)
3-183867959-C-G		not specified	Uncertain significance (Jan 23, 2024)
3-183868014-T-C		not specified	Uncertain significance (Oct 06, 2022)
3-183868032-C-T		not specified	Uncertain significance (Feb 28, 2023)
3-183884724-G-A			Likely benign (Nov 03, 2018)
3-183884725-C-A		not specified	Uncertain significance (Dec 16, 2023)
3-183884817-G-A			Likely benign (Nov 03, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PARL	protein_coding	protein_coding	ENST00000317096	10	55549

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000192	0.995	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0792	210	207	1.02	0.0000103	2458
Missense in Polyphen		31	38.298	0.80944		486
Synonymous	-1.42	91	75.3	1.21	0.00000409	727
Loss of Function	2.48	10	22.8	0.439	0.00000104	251

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000246	0.000239
Ashkenazi Jewish	0.00	0.00
East Asian	0.000353	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000353	0.000326
South Asian	0.0000653	0.0000653
Other	0.000662	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the control of apoptosis during postnatal growth. Essential for proteolytic processing of an antiapoptotic form of OPA1 which prevents the release of mitochondrial cytochrome c in response to intrinsic apoptoptic signals (By similarity). Promotes changes in mitochondria morphology regulated by phosphorylation of P-beta domain. {ECO:0000250, ECO:0000269|PubMed:14732705, ECO:0000269|PubMed:17116872}.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.925
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.76

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.197
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.481

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Parl
• Phenotype: cellular phenotype; muscle phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; respiratory system phenotype; immune system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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; hematopoietic system phenotype

Zebrafish Information Network

• Gene name: parlb
• Affected structure: caudal tuberculum
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: proteolysis;regulation of mitochondrion organization;regulation of proteolysis;membrane protein proteolysis;regulation of protein targeting to mitochondrion;regulation of reactive oxygen species metabolic process
• Cellular component: nucleus;mitochondrion;mitochondrial inner membrane;integral component of membrane
• Molecular function: endopeptidase activity;serine-type endopeptidase activity;protein binding