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.

• not_specified (151 variants)
• SH3D19-related_disorder (9 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
• not_provided (1 variants)
• Essential_tremor (1 variants)

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. These statistics are base on transcript: NM_001378122.1. 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				2		2
missense			93	9	2	104
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	93	11	2

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