SH3D19

SH3 domain containing 19

Basic information

Region (hg38): 4:151102751-151409365

Links

ENSG00000109686 ∙ NCBI:152503 ∙ OMIM:608674 ∙ HGNC:30418 ∙ Uniprot:Q5HYK7 ∙ 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 SH3D19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3D19 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			55	5		60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			29	5		34
Total	0	0	84	10	0

Variants in SH3D19

This is a list of pathogenic ClinVar variants found in the SH3D19 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-151102889-G-A		not specified	Uncertain significance (Nov 22, 2021)
4-151102899-A-G		not specified	Uncertain significance (Dec 28, 2022)
4-151103016-A-T		not specified	Uncertain significance (Aug 27, 2024)
4-151104535-C-A		not specified	Uncertain significance (Sep 16, 2021)
4-151104583-A-G		not specified	Uncertain significance (Apr 22, 2024)
4-151122116-T-C		not specified	Uncertain significance (Aug 14, 2024)
4-151122129-A-C		not specified	Uncertain significance (May 28, 2024)
4-151122195-T-C		not specified	Uncertain significance (Jun 04, 2024)
4-151127706-T-C		not specified	Uncertain significance (Sep 18, 2024)
4-151128206-C-T		not specified	Uncertain significance (Jun 26, 2024)
4-151128250-C-G		not specified	Uncertain significance (May 26, 2024)
4-151128274-C-G		not specified	Uncertain significance (Jun 27, 2023)
4-151128283-A-G		not specified	Uncertain significance (Aug 16, 2022)
4-151133066-T-A		SH3D19-related disorder	Likely benign (Nov 17, 2021)
4-151133069-A-G		not specified	Uncertain significance (May 31, 2024)
4-151133111-C-T		not specified	Uncertain significance (Sep 10, 2024)
4-151133154-G-T		not specified	Uncertain significance (Nov 21, 2022)
4-151133207-T-C		not specified	Uncertain significance (Dec 19, 2022)
4-151133216-C-G		not specified	Uncertain significance (Feb 07, 2023)
4-151133225-C-T		not specified	Uncertain significance (Jun 27, 2023)
4-151137758-A-G		not specified	Uncertain significance (Aug 23, 2021)
4-151137761-T-C		not specified	Likely benign (Mar 02, 2023)
4-151139804-T-A		not specified	Uncertain significance (Nov 11, 2024)
4-151139813-C-T		not specified	Uncertain significance (Apr 25, 2023)
4-151139835-C-A		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3D19	protein_coding	protein_coding	ENST00000304527	15	222882

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000556	1.00	125677	0	70	125747	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.583	385	419	0.920	0.0000207	5111
Missense in Polyphen		119	125.51	0.94811		1588
Synonymous	1.02	132	148	0.893	0.00000733	1601
Loss of Function	3.49	16	39.7	0.403	0.00000242	460

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00126	0.00125
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000195	0.000185
Middle Eastern	0.000218	0.000217
South Asian	0.000234	0.000229
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in regulating A disintegrin and metalloproteases (ADAMs) in the signaling of EGFR-ligand shedding. May be involved in suppression of Ras-induced cellular transformation and Ras-mediated activation of ELK1. Plays a role in the regulation of cell morphology and cytoskeletal organization. {ECO:0000269|PubMed:14551139, ECO:0000269|PubMed:15280379, ECO:0000269|PubMed:21834987}.
• Pathway: Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.732
• rvis_EVS: -0.09
• rvis_percentile_EVS: 47.12

Haploinsufficiency Scores

• pHI: 0.303
• hipred: Y
• hipred_score: 0.721
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.599

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3d19

Gene ontology

• Biological process: cytoskeleton organization;regulation of cell morphogenesis;positive regulation of membrane protein ectodomain proteolysis
• Cellular component: nucleoplasm;cytosol;plasma membrane
• Molecular function: protein binding