SH3GLB2

SH3 domain containing GRB2 like, endophilin B2, the group of N-BAR domain containing

Basic information

Region (hg38): 9:129007036-129028331

Links

ENSG00000148341 ∙ NCBI:56904 ∙ OMIM:609288 ∙ HGNC:10834 ∙ Uniprot:Q9NR46 ∙ 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 SH3GLB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3GLB2 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	1

Variants in SH3GLB2

This is a list of pathogenic ClinVar variants found in the SH3GLB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-129008745-A-G		not specified	Uncertain significance (Oct 17, 2023)
9-129008763-A-G		not specified	Uncertain significance (Nov 15, 2024)
9-129009146-T-C		not specified	Uncertain significance (Apr 23, 2024)
9-129009174-G-A		not specified	Uncertain significance (Apr 05, 2023)
9-129009339-C-T		not specified	Uncertain significance (Mar 21, 2023)
9-129009804-C-T		not specified	Uncertain significance (May 15, 2024)
9-129009861-A-G		not specified	Uncertain significance (Dec 21, 2022)
9-129010135-T-A			Benign (Apr 06, 2018)
9-129010152-G-A		not specified	Uncertain significance (Feb 14, 2024)
9-129010158-C-T		not specified	Uncertain significance (Nov 17, 2023)
9-129010169-C-T		not specified	Uncertain significance (Jun 19, 2024)
9-129010194-G-A		not specified	Uncertain significance (Mar 28, 2024)
9-129010209-C-G		not specified	Uncertain significance (Sep 01, 2024)
9-129012237-G-A		not specified	Uncertain significance (Sep 17, 2021)
9-129012244-C-T		not specified	Uncertain significance (Feb 05, 2024)
9-129012258-A-C		not specified	Uncertain significance (Jun 22, 2024)
9-129012258-A-T		not specified	Uncertain significance (Oct 03, 2022)
9-129012273-C-T		not specified	Uncertain significance (Dec 03, 2024)
9-129014413-T-C		not specified	Uncertain significance (Feb 16, 2023)
9-129014812-G-T		not specified	Uncertain significance (Sep 12, 2023)
9-129014835-G-A		not specified	Uncertain significance (Aug 02, 2022)
9-129014857-C-T		not specified	Uncertain significance (Jul 20, 2022)
9-129014872-T-C		not specified	Uncertain significance (May 02, 2024)
9-129021096-G-A		not specified	Uncertain significance (Apr 30, 2024)
9-129021105-G-A		not specified	Uncertain significance (Apr 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3GLB2	protein_coding	protein_coding	ENST00000372564	11	21268

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00149	0.992	125725	0	18	125743	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.38	159	216	0.735	0.0000129	2516
Missense in Polyphen		66	102.54	0.64366		1221
Synonymous	-1.06	104	91.2	1.14	0.00000579	781
Loss of Function	2.40	8	19.4	0.412	9.23e-7	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000294	0.0000294
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000167	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.487
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.203
• hipred: Y
• hipred_score: 0.739
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.791

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3glb2

Gene ontology

• Cellular component: nucleoplasm;cytoplasm;cytosol
• Molecular function: protein binding;identical protein binding;cadherin binding