SYPL2

synaptophysin like 2, the group of Synaptophysins|MARVEL domain containing

Basic information

Region (hg38): 1:109466546-109482134

Links

ENSG00000143028 ∙ NCBI:284612 ∙ ∙ HGNC:27638 ∙ Uniprot:Q5VXT5 ∙ 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 SYPL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYPL2 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in SYPL2

This is a list of pathogenic ClinVar variants found in the SYPL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-109466854-C-T		not specified	Uncertain significance (Mar 07, 2023)
1-109467083-C-T		not specified	Uncertain significance (May 05, 2023)
1-109467119-A-G		not specified	Uncertain significance (Aug 15, 2024)
1-109475582-T-C		not specified	Uncertain significance (Jun 05, 2023)
1-109475644-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-109476783-C-T		not specified	Uncertain significance (Dec 31, 2023)
1-109476784-G-A		not specified	Uncertain significance (Dec 27, 2022)
1-109476801-C-T		not specified	Uncertain significance (Aug 02, 2021)
1-109476853-T-A		not specified	Uncertain significance (Dec 18, 2023)
1-109476909-A-G		not specified	Uncertain significance (Mar 18, 2024)
1-109476933-C-T		not specified	Uncertain significance (Dec 16, 2022)
1-109476943-A-C		not specified	Uncertain significance (Aug 21, 2023)
1-109476956-G-A			Likely benign (Oct 01, 2022)
1-109476964-G-A		not specified	Uncertain significance (Dec 10, 2024)
1-109477831-C-T		not specified	Uncertain significance (Nov 30, 2022)
1-109477863-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-109477902-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-109477909-G-C		not specified	Uncertain significance (Nov 15, 2024)
1-109478007-G-A		not specified	Uncertain significance (Oct 11, 2024)
1-109479451-G-A		not specified	Uncertain significance (Jan 23, 2023)
1-109479528-G-A		not specified	Uncertain significance (Mar 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYPL2	protein_coding	protein_coding	ENST00000369872	6	15580

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000189	0.712	124772	0	29	124801	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.398	148	162	0.912	0.00000908	1779
Missense in Polyphen		67	69.156	0.96882		729
Synonymous	-0.164	69	67.3	1.03	0.00000419	532
Loss of Function	1.04	9	13.1	0.689	6.32e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000217	0.000216
Ashkenazi Jewish	0.00	0.00
East Asian	0.000612	0.000612
Finnish	0.00	0.00
European (Non-Finnish)	0.0000798	0.0000794
Middle Eastern	0.000612	0.000612
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in communication between the T-tubular and junctional sarcoplasmic reticulum (SR) membranes. {ECO:0000250}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.546
• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.7

Haploinsufficiency Scores

• pHI: 0.154
• hipred: N
• hipred_score: 0.296
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.141

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sypl2
• Phenotype: muscle phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: cellular calcium ion homeostasis;substantia nigra development
• Cellular component: synaptic vesicle;integral component of membrane