PDIK1L

PDLIM1 interacting kinase 1 like

Basic information

Region (hg38): 1:26111164-26125555

Links

ENSG00000175087 ∙ NCBI:149420 ∙ OMIM:610785 ∙ HGNC:18981 ∙ Uniprot:Q8N165 ∙ 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 PDIK1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDIK1L 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in PDIK1L

This is a list of pathogenic ClinVar variants found in the PDIK1L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-26114418-A-G		not specified	Uncertain significance (Apr 12, 2023)
1-26114504-A-T		not specified	Uncertain significance (Jan 03, 2022)
1-26114546-A-G		not specified	Uncertain significance (Apr 28, 2022)
1-26114549-G-A		not specified	Uncertain significance (Aug 08, 2023)
1-26122331-G-C		not specified	Uncertain significance (Mar 15, 2024)
1-26122445-A-C		not specified	Uncertain significance (Oct 20, 2023)
1-26122459-G-A		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDIK1L	protein_coding	protein_coding	ENST00000374271	2	14371

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.264	0.731	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.27	62	188	0.329	0.00000962	2263
Missense in Polyphen		12	80.098	0.14982		986
Synonymous	0.0784	66	66.8	0.988	0.00000356	655
Loss of Function	2.42	3	12.1	0.249	7.45e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000530	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.134
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.716
• hipred: Y
• hipred_score: 0.526
• ghis: 0.633

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.454

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdik1l

Gene ontology

• Biological process: protein phosphorylation;meiotic cell cycle
• Cellular component: nucleus;nucleoplasm
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding