PRELID2

PRELI domain containing 2, the group of PRELI domain containing

Basic information

Region (hg38): 5:145471799-145835369

Links

ENSG00000186314 ∙ NCBI:153768 ∙ ∙ HGNC:28306 ∙ Uniprot:Q8N945 ∙ 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 PRELID2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRELID2 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	14	0	0

Variants in PRELID2

This is a list of pathogenic ClinVar variants found in the PRELID2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-145764991-T-G		not specified	Uncertain significance (Dec 12, 2023)
5-145817918-C-G		not specified	Uncertain significance (Dec 03, 2021)
5-145817918-C-T		not specified	Uncertain significance (Jun 21, 2023)
5-145817919-G-A		not specified	Uncertain significance (Oct 05, 2021)
5-145817951-T-C		not specified	Uncertain significance (Jan 09, 2024)
5-145817955-T-C		not specified	Uncertain significance (May 11, 2022)
5-145817976-G-A		not specified	Uncertain significance (Jan 02, 2024)
5-145817979-T-G		not specified	Uncertain significance (May 18, 2022)
5-145819385-C-G		not specified	Uncertain significance (Dec 27, 2023)
5-145823122-T-A		not specified	Uncertain significance (Dec 21, 2023)
5-145835185-G-A		not specified	Uncertain significance (Mar 06, 2023)
5-145835190-C-G		not specified	Uncertain significance (Aug 01, 2022)
5-145835201-C-G		not specified	Uncertain significance (Jan 16, 2024)
5-145835239-C-T		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRELID2	protein_coding	protein_coding	ENST00000334744	7	363571

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.65e-9	0.142	125686	0	46	125732	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.284	88	95.8	0.918	0.00000479	1229
Missense in Polyphen		22	30.586	0.71929		421
Synonymous	0.870	26	32.3	0.805	0.00000159	334
Loss of Function	0.188	13	13.8	0.945	6.86e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000241
Ashkenazi Jewish	0.000500	0.000496
East Asian	0.000555	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000170	0.000167
Middle Eastern	0.000555	0.000544
South Asian	0.000197	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0948

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.181
• hipred: N
• hipred_score: 0.197
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prelid2
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

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