PEAK1

pseudopodium enriched atypical kinase 1

Basic information

Region (hg38): 15:77100656-77420144

Links

ENSG00000173517 ∙ NCBI:79834 ∙ OMIM:614248 ∙ HGNC:29431 ∙ Uniprot:Q9H792 ∙ 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 PEAK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEAK1 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			143	5		148
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	143	6	0

Variants in PEAK1

This is a list of pathogenic ClinVar variants found in the PEAK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-77114160-C-T		not specified	Uncertain significance (Dec 01, 2022)
15-77114185-A-C		not specified	Uncertain significance (May 24, 2024)
15-77114199-G-A		not specified	Uncertain significance (Feb 27, 2023)
15-77114203-T-A		not specified	Uncertain significance (Jan 30, 2024)
15-77114203-T-C		not specified	Uncertain significance (Jun 11, 2024)
15-77114233-A-C		not specified	Uncertain significance (Sep 14, 2022)
15-77114271-T-C		not specified	Uncertain significance (Sep 08, 2024)
15-77114348-G-A		PEAK1-related disorder	Likely benign (May 15, 2019)
15-77114383-C-T		not specified	Uncertain significance (Oct 06, 2023)
15-77114422-C-T		not specified	Uncertain significance (Oct 29, 2024)
15-77114449-G-C		not specified	Uncertain significance (Mar 20, 2024)
15-77114482-G-C		not specified	Uncertain significance (Jun 05, 2024)
15-77114505-C-A		not specified	Uncertain significance (Jan 23, 2023)
15-77114505-C-T		not specified	Uncertain significance (Jan 14, 2025)
15-77114621-C-T		PEAK1-related disorder	Likely benign (Mar 09, 2020)
15-77114629-A-G		not specified	Uncertain significance (Aug 28, 2024)
15-77114658-T-C		not specified	Uncertain significance (May 09, 2024)
15-77114677-G-C		not specified	Uncertain significance (May 24, 2024)
15-77114678-G-A		PEAK1-related disorder	Likely benign (May 15, 2019)
15-77114683-G-A		not specified	Uncertain significance (Nov 13, 2024)
15-77114798-G-C		PEAK1-related disorder	Likely benign (Aug 28, 2019)
15-77114812-G-C		not specified	Uncertain significance (Oct 09, 2024)
15-77114838-T-C		not specified	Uncertain significance (Sep 03, 2024)
15-77114846-T-C			Likely benign (Mar 01, 2023)
15-77114860-T-A		not specified	Uncertain significance (Aug 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PEAK1	protein_coding	protein_coding	ENST00000560626	4	312016

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000868	0.999	124766	0	45	124811	0.000180

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.177	940	925	1.02	0.0000498	11517
Missense in Polyphen		358	367.33	0.97461		4534
Synonymous	1.18	309	336	0.918	0.0000171	3471
Loss of Function	4.96	17	57.7	0.295	0.00000396	682

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000278	0.000278
Ashkenazi Jewish	0.000398	0.000397
East Asian	0.000447	0.000445
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000195	0.000177
Middle Eastern	0.000447	0.000445
South Asian	0.0000654	0.0000654
Other	0.000330	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable catalytically inactive kinase. Scaffolding protein that regulates the cytoskeleton to control cell spreading and migration by modulating focal adhesion dynamics (PubMed:23105102, PubMed:20534451). Acts as a scaffold for mediating EGFR signaling (PubMed:23846654). {ECO:0000269|PubMed:20534451, ECO:0000269|PubMed:23105102, ECO:0000269|PubMed:23846654}.

Intolerance Scores

• rvis_EVS: -1.29
• rvis_percentile_EVS: 5

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.756
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Peak1

Gene ontology

• Biological process: protein phosphorylation;cell migration;peptidyl-tyrosine phosphorylation;substrate adhesion-dependent cell spreading;protein autophosphorylation;focal adhesion assembly;regulation of focal adhesion assembly
• Cellular component: cytoplasm;focal adhesion;actin cytoskeleton
• Molecular function: protein kinase activity;non-membrane spanning protein tyrosine kinase activity;protein binding;ATP binding;identical protein binding