PAK1IP1

PAK1 interacting protein 1, the group of WD repeat domain containing

Basic information

Region (hg38): 6:10694972-10709782

Links

ENSG00000111845 ∙ NCBI:55003 ∙ OMIM:607811 ∙ HGNC:20882 ∙ Uniprot:Q9NWT1 ∙ 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 PAK1IP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAK1IP1 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in PAK1IP1

This is a list of pathogenic ClinVar variants found in the PAK1IP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-10695001-G-T		not specified	Uncertain significance (Dec 04, 2024)
6-10695041-C-G		not specified	Uncertain significance (Jan 16, 2024)
6-10697331-C-T		not specified	Uncertain significance (Mar 20, 2024)
6-10697347-C-A		not specified	Uncertain significance (Jan 31, 2024)
6-10697351-C-T		not specified	Uncertain significance (Mar 24, 2023)
6-10697355-A-G		not specified	Uncertain significance (Jun 06, 2023)
6-10697397-G-A		not specified	Uncertain significance (May 30, 2023)
6-10697397-G-C		not specified	Uncertain significance (Jul 05, 2023)
6-10697402-G-T		not specified	Uncertain significance (Jul 05, 2023)
6-10697435-A-G		not specified	Uncertain significance (Nov 03, 2023)
6-10697439-A-G		not specified	Uncertain significance (Mar 23, 2022)
6-10697448-A-G		not specified	Uncertain significance (Aug 16, 2022)
6-10702431-C-T		not specified	Uncertain significance (Aug 11, 2024)
6-10702437-T-C		not specified	Uncertain significance (Jan 23, 2025)
6-10702446-G-C		not specified	Uncertain significance (Jan 30, 2024)
6-10702468-T-C		not specified	Uncertain significance (Nov 17, 2022)
6-10702572-G-T		not specified	Uncertain significance (Apr 12, 2024)
6-10702576-C-G		not specified	Uncertain significance (Nov 24, 2024)
6-10702590-C-T		not specified	Uncertain significance (Feb 22, 2025)
6-10702608-G-A		not specified	Uncertain significance (Dec 30, 2023)
6-10702624-C-A		not specified	Uncertain significance (Oct 25, 2024)
6-10703443-A-G		not specified	Uncertain significance (Mar 06, 2023)
6-10704541-G-C		not specified	Uncertain significance (Nov 10, 2024)
6-10704578-T-A		not specified	Uncertain significance (May 20, 2024)
6-10704578-T-C		not specified	Uncertain significance (Aug 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAK1IP1	protein_coding	protein_coding	ENST00000379568	10	15088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.363	0.637	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.827	173	206	0.838	0.00000986	2593
Missense in Polyphen		44	55.294	0.79575		702
Synonymous	0.179	70	71.9	0.973	0.00000363	711
Loss of Function	3.02	4	17.7	0.226	7.46e-7	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000431	0.000431
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000798	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates the PAK1 kinase. PAK1 is a member of the PAK kinase family, which has been shown to play a positive role in the regulation of signaling pathways involving MAPK8 and RELA. PAK1 exists as an inactive homodimer, which is activated by binding of small GTPases such as CDC42 to an N-terminal regulatory domain. PAK1IP1 also binds to the N-terminus of PAK1, and inhibits the specific activation of PAK1 by CDC42. May be involved in ribosomal large subunit assembly (PubMed:24120868). {ECO:0000269|PubMed:11371639, ECO:0000269|PubMed:24120868}.
• Pathway: EGF-Ncore (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.567
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.596
• hipred: Y
• hipred_score: 0.802
• ghis: 0.522

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.954

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pak1ip1
• Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; craniofacial phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; skeleton phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: cell population proliferation;negative regulation of signal transduction;ribosomal large subunit biogenesis;roof of mouth development;regulation of signal transduction by p53 class mediator
• Cellular component: nucleolus
• Molecular function: protein binding