SYNPR

synaptoporin, the group of Synaptophysins|MARVEL domain containing

Basic information

Region (hg38): 3:63228314-63616924

Links

ENSG00000163630 ∙ NCBI:132204 ∙ ∙ HGNC:16507 ∙ Uniprot:Q8TBG9 ∙ 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 SYNPR gene.

• Inborn genetic diseases (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNPR 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in SYNPR

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

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

Position	Type	Phenotype	Significance	ClinVar
3-63278698-C-T		not specified	Uncertain significance (Mar 27, 2023)
3-63278702-T-A		not specified	Uncertain significance (May 31, 2023)
3-63278729-G-A		not specified	Uncertain significance (Sep 12, 2023)
3-63480854-C-T		not specified	Uncertain significance (Jan 29, 2024)
3-63480862-G-A		not specified	Uncertain significance (Nov 17, 2022)
3-63480901-G-A		not specified	Uncertain significance (Aug 30, 2022)
3-63480947-A-G		not specified	Uncertain significance (May 27, 2022)
3-63556640-G-A		not specified	Uncertain significance (Jul 19, 2022)
3-63556668-A-G		not specified	Uncertain significance (Apr 28, 2022)
3-63556716-G-A		not specified	Uncertain significance (Feb 06, 2024)
3-63556725-A-C		not specified	Uncertain significance (Aug 16, 2021)
3-63609215-G-T		not specified	Uncertain significance (Jan 09, 2024)
3-63615248-C-G		not specified	Uncertain significance (Jan 23, 2023)
3-63615287-G-A		not specified	Uncertain significance (Apr 05, 2023)
3-63615296-T-G		not specified	Uncertain significance (Nov 08, 2022)
3-63615323-C-T		not specified	Uncertain significance (Dec 19, 2022)
3-63615428-G-T		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNPR	protein_coding	protein_coding	ENST00000478300	6	388607

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00419	0.965	124626	0	8	124634	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.419	141	156	0.905	0.00000860	1834
Missense in Polyphen		46	59.223	0.77672		767
Synonymous	-0.793	73	64.9	1.13	0.00000404	558
Loss of Function	1.89	6	13.5	0.446	5.70e-7	168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000956	0.0000956
Ashkenazi Jewish	0.000102	0.0000994
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.0000672	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Intrinsic membrane protein of small synaptic vesicles. Probable vesicular channel protein (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.510
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.0510
• hipred: N
• hipred_score: 0.287
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.159

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Synpr
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Cellular component: cell junction;integral component of synaptic vesicle membrane;neuron projection
• Molecular function: protein binding