PCP4L1

Purkinje cell protein 4 like 1

Basic information

Region (hg38): 1:161258745-161285450

Links

ENSG00000248485 ∙ NCBI:654790 ∙ ∙ HGNC:20448 ∙ Uniprot:A6NKN8 ∙ 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 PCP4L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCP4L1 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	4	0	2

Variants in PCP4L1

This is a list of pathogenic ClinVar variants found in the PCP4L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-161283731-G-T			Benign (Jul 23, 2018)
1-161284363-C-T		not specified	Uncertain significance (Aug 13, 2021)
1-161284366-A-C		not specified	Uncertain significance (Oct 01, 2024)
1-161284443-C-T		not specified	Uncertain significance (Dec 14, 2023)
1-161284444-G-A		not specified	Uncertain significance (Dec 28, 2022)
1-161284466-G-A			Benign (Jul 23, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCP4L1	protein_coding	protein_coding	ENST00000504449	3	26724

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0527	0.713	124633	0	5	124638	0.0000201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0835	35	36.4	0.961	0.00000186	441
Missense in Polyphen		23	24.991	0.92033		291
Synonymous	-0.00241	13	13.0	1.00	6.44e-7	121
Loss of Function	0.706	2	3.41	0.587	1.44e-7	44

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000610	0.0000610
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000272	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.453
• rvis_EVS: 0.32
• rvis_percentile_EVS: 72.94

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.208
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcp4l1