SYNPR

protein-coding

synaptoporin, the group of Synaptophysins|MARVEL domain containing

Gene summary

Predicted to be involved in modulation of chemical synaptic transmission. Predicted to be located in membrane; neuron projection; and synaptic vesicle. Predicted to be active in hippocampal mossy fiber to CA3 synapse and synaptic vesicle membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001130003.2

Inheritance

—

ClinVar variants

U:35B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr3:63,228,315-63,616,924

External References & Databases

Ensembl (ENSG00000163630)

Transcript & Mutation Effects

hg38 • Region Span ~388.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SYNPR variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 36

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001130003.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			35 clinvar			35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	35	1	0	36

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001130003.2	RefSeq	NP_001123475.1	6	MANE Select
ENST00000478300.6	Ensembl	ENSP00000418994.1	6	MANE Select
NM_144642.5	RefSeq	NP_653243.1	5	Standard
ENST00000295894.10	Ensembl	ENSP00000295894.5	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

cell junction
integral component of synaptic vesicle membrane
neuron projection

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000478300
Coding exons: 6
Length: 388607
Individuals with no LoFs: 124626
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 124634
p: 0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.419	141	156	0.905	0.00000860	1834
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000031	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000027	rare
South Asian	0.000067	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.159

Gene Damage Prediction

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