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.

• not_specified (89 variants)

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. These statistics are base on transcript: NM_000138392.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			87	1		88
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	87	2	0

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