SHCBP1

SHC binding and spindle associated 1

Basic information

Region (hg38): 16:46578591-46621379

Links

ENSG00000171241 ∙ NCBI:79801 ∙ OMIM:611027 ∙ HGNC:29547 ∙ Uniprot:Q8NEM2 ∙ 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 SHCBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHCBP1 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			42	2	1	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	2	1

Variants in SHCBP1

This is a list of pathogenic ClinVar variants found in the SHCBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-46581793-A-G		not specified	Uncertain significance (Jul 13, 2021)
16-46581832-G-A		not specified	Uncertain significance (Sep 01, 2024)
16-46581892-A-G		not specified	Uncertain significance (Sep 14, 2022)
16-46581949-G-A		not specified	Uncertain significance (Apr 07, 2022)
16-46581976-C-T		not specified	Uncertain significance (Nov 15, 2024)
16-46581986-G-T		not specified	Uncertain significance (Feb 10, 2023)
16-46581992-C-T		not specified	Uncertain significance (May 04, 2022)
16-46582045-G-A		not specified	Uncertain significance (Sep 14, 2023)
16-46583524-C-G		not specified	Uncertain significance (Dec 06, 2024)
16-46583563-G-A		not specified	Uncertain significance (Mar 28, 2023)
16-46583566-T-C		not specified	Uncertain significance (Jan 26, 2022)
16-46583588-C-T		not specified	Uncertain significance (Jul 05, 2024)
16-46583593-T-C		not specified	Uncertain significance (May 30, 2024)
16-46583606-T-C		not specified	Likely benign (May 04, 2023)
16-46584013-A-G		not specified	Uncertain significance (Nov 13, 2023)
16-46584037-C-T		not specified	Uncertain significance (Dec 01, 2022)
16-46584088-C-T		not specified	Uncertain significance (Oct 05, 2023)
16-46595562-T-C		not specified	Uncertain significance (Apr 18, 2023)
16-46595577-T-A		not specified	Uncertain significance (Jan 23, 2023)
16-46595583-A-T		not specified	Uncertain significance (Dec 14, 2022)
16-46595586-A-G		not specified	Uncertain significance (Sep 09, 2021)
16-46595661-C-T		not specified	Uncertain significance (Dec 04, 2024)
16-46595662-G-A		not specified	Uncertain significance (Oct 06, 2024)
16-46595668-C-T		not specified	Likely benign (Apr 04, 2024)
16-46595670-A-G		not specified	Uncertain significance (May 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHCBP1	protein_coding	protein_coding	ENST00000303383	13	41073

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.38e-8	0.996	125646	0	101	125747	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	295	359	0.822	0.0000179	4445
Missense in Polyphen		56	87.806	0.63777		1116
Synonymous	1.77	110	136	0.808	0.00000719	1233
Loss of Function	2.61	17	33.3	0.511	0.00000164	416

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000718	0.000716
Ashkenazi Jewish	0.00	0.00
East Asian	0.000719	0.000707
Finnish	0.000237	0.000231
European (Non-Finnish)	0.000448	0.000440
Middle Eastern	0.000719	0.000707
South Asian	0.000458	0.000457
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in signaling pathways governing cellular proliferation, cell growth and differentiation. May be a component of a novel signaling pathway downstream of Shc. Acts as a positive regulator of FGF signaling in neural progenitor cells. {ECO:0000250|UniProtKB:Q9Z179}.

Recessive Scores

• pRec: 0.0996

Intolerance Scores

• loftool: 0.850
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.65

Haploinsufficiency Scores

• pHI: 0.331
• hipred: Y
• hipred_score: 0.523
• ghis: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.168

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Shcbp1
• Phenotype: immune system phenotype; hematopoietic system phenotype; normal phenotype

Gene ontology

• Biological process: fibroblast growth factor receptor signaling pathway;regulation of neural precursor cell proliferation
• Cellular component: cytoplasm;spindle;midbody
• Molecular function: protein binding;SH2 domain binding