PDZK1IP1

PDZK1 interacting protein 1

Basic information

Region (hg38): 1:47183582-47191044

Links

ENSG00000162366 ∙ NCBI:10158 ∙ OMIM:607178 ∙ HGNC:16887 ∙ Uniprot:Q13113 ∙ 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 PDZK1IP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDZK1IP1 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	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in PDZK1IP1

This is a list of pathogenic ClinVar variants found in the PDZK1IP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-47183987-C-T		not specified	Uncertain significance (Dec 11, 2023)
1-47184004-C-A		not specified	Uncertain significance (Jan 10, 2025)
1-47184006-C-T		not specified	Uncertain significance (Jan 18, 2025)
1-47184033-G-A		not specified	Uncertain significance (Oct 20, 2023)
1-47185011-G-A		not specified	Uncertain significance (Jul 16, 2024)
1-47185014-G-A		not specified	Uncertain significance (Feb 23, 2025)
1-47185053-C-T		not specified	Uncertain significance (Jan 10, 2022)
1-47185069-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-47185093-G-C		not specified	Uncertain significance (Jan 20, 2025)
1-47187320-G-T		not specified	Uncertain significance (Dec 12, 2023)
1-47187388-G-A		not specified	Uncertain significance (Mar 07, 2024)
1-47187417-G-T		not specified	Likely benign (Oct 19, 2024)
1-47189898-A-C		not specified	Uncertain significance (Mar 07, 2025)
1-47189913-A-G		not specified	Uncertain significance (Oct 08, 2024)
1-47189917-G-A		not specified	Uncertain significance (May 31, 2023)
1-47189925-G-A		not specified	Uncertain significance (Feb 07, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDZK1IP1	protein_coding	protein_coding	ENST00000294338	4	7452

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000918	0.589	125042	0	23	125065	0.0000920

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.422	59	68.8	0.857	0.00000402	730
Missense in Polyphen		18	22.115	0.81391		246
Synonymous	-0.921	38	31.4	1.21	0.00000226	226
Loss of Function	0.484	5	6.31	0.792	3.70e-7	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000124
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000327
Finnish	0.00	0.00
European (Non-Finnish)	0.0000891	0.0000887
Middle Eastern	0.000327	0.000327
South Asian	0.000131	0.000131
Other	0.000164	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in tumor biology.

Recessive Scores

• pRec: 0.255

Intolerance Scores

• loftool: 0.442
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.541
• hipred: N
• hipred_score: 0.310
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdzk1ip1

Zebrafish Information Network

• Gene name: pdzk1ip1
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Cellular component: integral component of membrane;extracellular exosome