PRELID3A

PRELI domain containing 3A, the group of PRELI domain containing

Basic information

Region (hg38): 18:12407896-12432238

Previous symbols: [ "C18orf43", "SLMO1" ]

Links

ENSG00000141391 ∙ NCBI:10650 ∙ OMIM:616545 ∙ HGNC:24639 ∙ Uniprot:Q96N28 ∙ 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 PRELID3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRELID3A 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			9			9
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	9	0	0

Variants in PRELID3A

This is a list of pathogenic ClinVar variants found in the PRELID3A region.

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

Position	Type	Phenotype	Significance	ClinVar
18-12407992-C-T		not specified	Uncertain significance (Dec 09, 2024)
18-12408000-G-A		not specified	Uncertain significance (Dec 02, 2022)
18-12420325-C-T		not specified	Likely benign (Oct 25, 2023)
18-12420348-A-T		not specified	Uncertain significance (Dec 07, 2023)
18-12420424-C-G		not specified	Uncertain significance (Sep 23, 2023)
18-12420444-G-A		not specified	Uncertain significance (May 17, 2023)
18-12427069-A-G		not specified	Uncertain significance (Apr 13, 2022)
18-12427232-C-T		not specified	Uncertain significance (Jul 05, 2023)
18-12429382-C-G		not specified	Uncertain significance (Feb 16, 2023)
18-12429383-T-C		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRELID3A	protein_coding	protein_coding	ENST00000440960	6	24343

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.67e-9	0.0342	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.456	82	94.5	0.868	0.00000457	1111
Missense in Polyphen		36	42.914	0.83888		494
Synonymous	-0.407	40	36.9	1.09	0.00000196	327
Loss of Function	-0.769	12	9.45	1.27	4.87e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000119	0.000114
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: In vitro, the TRIAP1:PRELID3A complex mediates the transfer of phosphatidic acid (PA) between liposomes and probably functions as a PA transporter across the mitochondrion intermembrane space. Phosphatidic acid import is required for cardiolipin (CL) synthesis in the mitochondrial inner membrane. {ECO:0000305|PubMed:26071602}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;TP53 Regulates Transcription of Genes Involved in Cytochrome C Release;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

• pHI: 0.238
• hipred: N
• hipred_score: 0.352
• ghis: 0.623

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Prelid3a

Gene ontology

• Biological process: phospholipid transport
• Cellular component: mitochondrial intermembrane space
• Molecular function: protein binding;phosphatidic acid transporter activity