SHKBP1

SH3KBP1 binding protein 1, the group of WD repeat domain containing

Basic information

Region (hg38): 19:40576853-40591399

Links

ENSG00000160410 ∙ NCBI:92799 ∙ OMIM:617322 ∙ HGNC:19214 ∙ Uniprot:Q8TBC3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SHKBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHKBP1 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			60	1		61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	60	2	0

Variants in SHKBP1

This is a list of pathogenic ClinVar variants found in the SHKBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-40576913-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-40576949-C-A		not specified	Uncertain significance (Mar 29, 2023)
19-40577245-G-T		not specified	Uncertain significance (Oct 25, 2022)
19-40577259-T-G		not specified	Uncertain significance (Apr 12, 2022)
19-40577406-G-A		not specified	Uncertain significance (Jul 05, 2023)
19-40577435-C-T		not specified	Likely benign (Jun 10, 2024)
19-40577619-G-T		not specified	Uncertain significance (Oct 27, 2022)
19-40577626-C-T		not specified	Uncertain significance (Aug 04, 2023)
19-40578156-G-T		not specified	Uncertain significance (Nov 27, 2023)
19-40578164-G-A		not specified	Uncertain significance (Oct 28, 2024)
19-40578168-C-A		not specified	Uncertain significance (Jun 22, 2021)
19-40578204-C-G		not specified	Uncertain significance (Aug 14, 2024)
19-40578522-A-G		not specified	Uncertain significance (Mar 04, 2025)
19-40578524-G-T		not specified	Uncertain significance (Feb 26, 2025)
19-40580347-C-T		not specified	Uncertain significance (Jan 30, 2024)
19-40580383-C-T		not specified	Uncertain significance (Nov 10, 2022)
19-40580450-G-A		not specified	Uncertain significance (Aug 11, 2024)
19-40580470-C-T		not specified	Uncertain significance (Mar 01, 2024)
19-40580479-C-T		not specified	Uncertain significance (Jun 16, 2023)
19-40580649-T-G		not specified	Uncertain significance (Feb 22, 2023)
19-40580787-C-T		not specified	Uncertain significance (Jan 30, 2024)
19-40580790-G-A		not specified	Uncertain significance (Nov 10, 2022)
19-40580919-G-A		not specified	Uncertain significance (Jun 30, 2023)
19-40580921-G-A		not specified	Likely benign (Feb 02, 2024)
19-40582368-G-A		not specified	Uncertain significance (Jan 23, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHKBP1	protein_coding	protein_coding	ENST00000291842	18	14549

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.81e-8	0.999	125649	0	99	125748	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.98	343	463	0.741	0.0000311	4494
Missense in Polyphen		80	121.9	0.65628		1155
Synonymous	0.127	190	192	0.988	0.0000130	1518
Loss of Function	2.91	18	37.2	0.484	0.00000199	378

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00144	0.00143
Ashkenazi Jewish	0.00	0.00
East Asian	0.000439	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000284	0.000281
Middle Eastern	0.000439	0.000435
South Asian	0.000512	0.000490
Other	0.000493	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits CBL-SH3KBP1 complex mediated down-regulation of EGFR signaling by sequestration of SH3KBP1. Binds to SH3KBP1 and prevents its interaction with CBL and inhibits translocation of SH3KBP1 to EGFR containing vesicles upon EGF stimulation. {ECO:0000250|UniProtKB:Q6P7W2}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.791
• rvis_EVS: -1.17
• rvis_percentile_EVS: 6.03

Haploinsufficiency Scores

• pHI: 0.274
• hipred: Y
• hipred_score: 0.637
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.970

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Shkbp1

Gene ontology

• Biological process: positive regulation of epidermal growth factor receptor signaling pathway;protein homooligomerization
• Cellular component: lysosome
• Molecular function: protein binding