SHB

SH2 domain containing adaptor protein B, the group of SH2 domain containing

Basic information

Region (hg38): 9:37915898-38069227

Links

ENSG00000107338 ∙ NCBI:6461 ∙ OMIM:600314 ∙ HGNC:10838 ∙ Uniprot:Q15464 ∙ 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 SHB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHB 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				2	3	5
missense			45	1		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	3	3

Variants in SHB

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

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

Position	Type	Phenotype	Significance	ClinVar
9-37919842-G-A			Benign (May 24, 2018)
9-37919925-C-T		not specified	Uncertain significance (Apr 25, 2023)
9-37919929-C-T			Benign (May 24, 2018)
9-37919980-C-T		not specified	Uncertain significance (Nov 27, 2023)
9-37948648-A-C		not specified	Uncertain significance (Apr 18, 2023)
9-37948655-A-T		not specified	Uncertain significance (Jan 27, 2022)
9-37948738-T-C		not specified	Uncertain significance (Oct 12, 2021)
9-37955922-C-T		not specified	Uncertain significance (Feb 03, 2023)
9-37955985-C-A		not specified	Uncertain significance (Oct 26, 2022)
9-37955998-G-A		not specified	Uncertain significance (Nov 03, 2023)
9-37956040-T-G		not specified	Uncertain significance (Mar 15, 2024)
9-37974645-C-T		not specified	Uncertain significance (Nov 17, 2023)
9-37974661-G-A		not specified	Uncertain significance (Jul 15, 2021)
9-37974679-C-T		not specified	Uncertain significance (Aug 17, 2021)
9-37974689-G-A		not specified	Likely benign (Oct 25, 2023)
9-37974707-G-C		not specified	Uncertain significance (Dec 19, 2022)
9-37974715-G-A		not specified	Uncertain significance (Dec 07, 2021)
9-38016063-C-A		not specified	Uncertain significance (Oct 12, 2022)
9-38016095-C-A		not specified	Uncertain significance (May 13, 2024)
9-38067930-T-C		not specified	Uncertain significance (Apr 14, 2023)
9-38067931-T-C		not specified	Uncertain significance (Aug 08, 2023)
9-38067949-C-T		not specified	Uncertain significance (Feb 05, 2024)
9-38067952-T-C		not specified	Uncertain significance (May 08, 2024)
9-38067958-C-T		not specified	Uncertain significance (Jan 04, 2024)
9-38067960-G-C		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHB	protein_coding	protein_coding	ENST00000377707	6	150080

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.969	0.0313	124814	0	3	124817	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.241	246	257	0.958	0.0000148	3164
Missense in Polyphen		57	81.636	0.69822		927
Synonymous	0.447	102	108	0.945	0.00000667	991
Loss of Function	3.68	2	19.6	0.102	9.21e-7	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.00000885	0.00000883
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein which regulates several signal transduction cascades by linking activated receptors to downstream signaling components. May play a role in angiogenesis by regulating FGFR1, VEGFR2 and PDGFR signaling. May also play a role in T-cell antigen receptor/TCR signaling, interleukin-2 signaling, apoptosis and neuronal cells differentiation by mediating basic- FGF and NGF-induced signaling cascades. May also regulate IRS1 and IRS2 signaling in insulin-producing cells. {ECO:0000269|PubMed:10828022, ECO:0000269|PubMed:10837138, ECO:0000269|PubMed:12084069, ECO:0000269|PubMed:12464388, ECO:0000269|PubMed:12520086, ECO:0000269|PubMed:15026417, ECO:0000269|PubMed:15919073, ECO:0000269|PubMed:8806685, ECO:0000269|PubMed:9484780, ECO:0000269|PubMed:9751119}.
• Pathway: Angiogenesis overview;VEGFA-VEGFR2 Signaling Pathway;Signal Transduction;VEGFA-VEGFR2 Pathway;TCR;EGFR1;IL2;Signaling by VEGF;Signaling by Receptor Tyrosine Kinases;Signaling events mediated by VEGFR1 and VEGFR2;PDGFR-alpha signaling pathway (Consensus)

Recessive Scores

• pRec: 0.121

Haploinsufficiency Scores

• pHI: 0.320
• hipred: Y
• hipred_score: 0.741
• ghis: 0.438

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.655

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Shb
• Phenotype: limbs/digits/tail 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system 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); embryo phenotype

Gene ontology

• Biological process: angiogenesis;apoptotic process;signal transduction;positive regulation of signal transduction;cell differentiation;vascular endothelial growth factor receptor signaling pathway
• Cellular component: nucleoplasm;cytosol;plasma membrane;cytoplasmic ribonucleoprotein granule
• Molecular function: phosphotyrosine residue binding;SH3/SH2 adaptor activity;protein binding