SH3YL1

SH3 and SYLF domain containing 1

Basic information

Region (hg38): 2:217730-266398

Links

ENSG00000035115 ∙ NCBI:26751 ∙ OMIM:617314 ∙ HGNC:29546 ∙ Uniprot:Q96HL8 ∙ 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 SH3YL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3YL1 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in SH3YL1

This is a list of pathogenic ClinVar variants found in the SH3YL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-218819-T-C		not specified	Uncertain significance (Jun 17, 2024)
2-218888-A-G		not specified	Uncertain significance (Jun 02, 2023)
2-218902-A-G		not specified	Uncertain significance (Jan 05, 2022)
2-218971-G-A		not specified	Uncertain significance (Dec 14, 2021)
2-218982-T-C		not specified	Uncertain significance (Feb 16, 2023)
2-218984-T-C		not specified	Uncertain significance (Oct 10, 2023)
2-229983-A-T		not specified	Uncertain significance (Mar 20, 2024)
2-230011-G-A		not specified	Uncertain significance (Oct 03, 2023)
2-231066-C-T		not specified	Uncertain significance (Aug 13, 2021)
2-231115-A-G		not specified	Uncertain significance (Jun 18, 2021)
2-231124-C-T		not specified	Uncertain significance (May 29, 2024)
2-231127-C-T		not specified	Uncertain significance (Feb 17, 2022)
2-231136-G-T		not specified	Uncertain significance (Apr 07, 2022)
2-231138-C-T		not specified	Uncertain significance (Jan 23, 2023)
2-231139-G-A		not specified	Uncertain significance (May 03, 2023)
2-231144-G-A		not specified	Likely benign (Oct 31, 2023)
2-231161-G-T		not specified	Uncertain significance (Jan 02, 2024)
2-233182-G-A		not specified	Uncertain significance (Feb 03, 2022)
2-233183-T-G		not specified	Uncertain significance (Apr 20, 2023)
2-233200-C-T		not specified	Uncertain significance (May 14, 2024)
2-233213-C-A		not specified	Uncertain significance (Feb 28, 2024)
2-233215-T-G		not specified	Uncertain significance (Oct 17, 2023)
2-233229-C-A		not specified	Uncertain significance (Sep 12, 2023)
2-234197-C-T		not specified	Uncertain significance (Dec 19, 2023)
2-234239-G-A		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3YL1	protein_coding	protein_coding	ENST00000356150	10	48669

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.37e-8	0.648	124488	3	303	124794	0.00123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.501	163	182	0.895	0.00000988	2190
Missense in Polyphen		65	69.969	0.92898		802
Synonymous	0.893	62	71.6	0.866	0.00000445	685
Loss of Function	1.19	14	19.7	0.711	0.00000107	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00146	0.00146
Ashkenazi Jewish	0.000606	0.000596
East Asian	0.000890	0.000890
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000599	0.000583
Middle Eastern	0.000890	0.000890
South Asian	0.00538	0.00524
Other	0.00206	0.00198

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.188

Intolerance Scores

• loftool: 0.852
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• pHI: 0.270
• hipred: N
• hipred_score: 0.333
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.760

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3yl1

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;regulation of ruffle assembly
• Cellular component: ruffle membrane
• Molecular function: protein binding;phosphatase binding;phosphatidylinositol binding