SYPL1

synaptophysin like 1, the group of MARVEL domain containing|Synaptophysins

Basic information

Region (hg38): 7:106090505-106112589

Previous symbols: [ "SYPL" ]

Links

ENSG00000008282 ∙ ∙ OMIM:616665 ∙ HGNC:11507 ∙ Uniprot:Q16563 ∙ 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 SYPL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYPL1 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in SYPL1

This is a list of pathogenic ClinVar variants found in the SYPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-106091837-G-C		not specified	Uncertain significance (Nov 10, 2022)
7-106091857-T-C		not specified	Uncertain significance (May 31, 2024)
7-106092999-G-C		not specified	Uncertain significance (Mar 21, 2023)
7-106093022-G-A		not specified	Uncertain significance (May 23, 2024)
7-106093047-C-T		not specified	Uncertain significance (Aug 28, 2024)
7-106097707-G-A		not specified	Uncertain significance (Mar 07, 2024)
7-106097727-G-T		not specified	Uncertain significance (Feb 02, 2025)
7-106097737-C-A		not specified	Uncertain significance (May 30, 2024)
7-106097766-A-G		not specified	Uncertain significance (Oct 24, 2023)
7-106097834-A-T		not specified	Uncertain significance (Nov 15, 2024)
7-106099192-T-C		not specified	Uncertain significance (Mar 10, 2025)
7-106099210-G-A		not specified	Uncertain significance (Feb 19, 2025)
7-106099228-T-A		not specified	Uncertain significance (Feb 28, 2024)
7-106099228-T-C		not specified	Uncertain significance (Oct 20, 2024)
7-106099254-C-T		Intellectual disability	Uncertain significance (Oct 16, 2020)
7-106112172-C-T		not specified	Uncertain significance (Oct 06, 2021)
7-106112493-T-C		not specified	Uncertain significance (Feb 14, 2023)
7-106112511-A-C		not specified	Uncertain significance (Feb 09, 2023)
7-106112516-A-C		not specified	Uncertain significance (Aug 29, 2024)
7-106112517-T-A		not specified	Uncertain significance (Jun 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYPL1	protein_coding	protein_coding	ENST00000011473	6	22074

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0467	0.931	125707	0	7	125714	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.447	120	135	0.891	0.00000635	1680
Missense in Polyphen		38	53.359	0.71216		700
Synonymous	0.253	48	50.3	0.955	0.00000258	518
Loss of Function	1.99	4	11.2	0.358	4.76e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.627
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.338
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.704

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sypl
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype

Gene ontology

• Biological process: chemical synaptic transmission
• Cellular component: integral component of plasma membrane;integral component of membrane;secretory granule;integral component of synaptic vesicle membrane;melanosome;extracellular exosome