SYNGR4

Summary

SYNGR4 (synaptogyrin 4, HGNC:11502) is a protein-coding gene on chromosome 19q13.33, encoding Synaptogyrin-4 (O95473).

This gene encodes an integral membrane protein. The gene belongs to the synaptogyrin gene family. Like other members of the family the protein contains four transmembrane regions. The exact function of this protein is unclear.

Source: NCBI Gene 23546 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 50 total
• MANE Select transcript: NM_012451

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11502
Approved symbol	SYNGR4
Name	synaptogyrin 4
Location	19q13.33
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000105467
Ensembl biotype	protein_coding
OMIM	608373
Entrez	23546

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000344846, ENST00000595322, ENST00000600863, ENST00000601610

RefSeq mRNA: 1 — MANE Select: NM_012451 NM_012451

CCDS: CCDS12717

Canonical transcript exons

ENST00000344846 — 5 exons

Exon	Start	End
ENSE00000717516	48375613	48375752
ENSE00000853308	48376085	48376377
ENSE00001251105	48364367	48364537
ENSE00001364762	48365736	48365935
ENSE00003464879	48373517	48373754

Expression profiles

Bgee: expression breadth ubiquitous, 116 present calls, max score 93.01.

FANTOM5 (CAGE): breadth broad, TPM avg 0.5169 / max 105.3291, expressed in 188 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter ID	TPM avg	Samples expressed
176769	0.3082	146
176767	0.0487	4
176774	0.0287	6
176768	0.0276	6
176776	0.0218	4
176771	0.0167	7
176772	0.0157	6
176770	0.0147	5
176773	0.0118	5
176778	0.0093	1

Top tissues by expression

266 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	93.01	gold quality
left testis	UBERON:0004533	92.74	gold quality
testis	UBERON:0000473	89.85	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.34	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.01	gold quality
islet of Langerhans	UBERON:0000006	75.31	gold quality
cerebellar cortex	UBERON:0002129	74.34	gold quality
cerebellar hemisphere	UBERON:0002245	74.29	gold quality
buccal mucosa cell	CL:0002336	73.52	gold quality
adult organism	UBERON:0007023	73.26	gold quality
right hemisphere of cerebellum	UBERON:0014890	73.02	gold quality
cerebellum	UBERON:0002037	72.56	gold quality
endometrium epithelium	UBERON:0004811	71.68	gold quality
paraflocculus	UBERON:0005351	71.13	gold quality
frontal pole	UBERON:0002795	70.57	gold quality
middle frontal gyrus	UBERON:0002702	70.03	gold quality
Brodmann (1909) area 10	UBERON:0013541	67.06	gold quality
pancreas	UBERON:0001264	60.79	gold quality
cerebellar vermis	UBERON:0004720	60.29	gold quality
prefrontal cortex	UBERON:0000451	57.81	gold quality
epithelial cell of pancreas	CL:0000083	56.52	gold quality
ileal mucosa	UBERON:0000331	56.19	silver quality
body of pancreas	UBERON:0001150	55.28	gold quality
tibia	UBERON:0000979	54.44	gold quality
tibialis anterior	UBERON:0001385	54.23	silver quality
frontal cortex	UBERON:0001870	53.98	gold quality
quadriceps femoris	UBERON:0001377	53.52	gold quality
neocortex	UBERON:0001950	52.66	gold quality
thymus	UBERON:0002370	52.64	gold quality
vastus lateralis	UBERON:0001379	52.40	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ENAD-27	no	96.81
E-ANND-3	no	1.02

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Syngr4	ENSMUSG00000040231
rattus_norvegicus	Syngr4	ENSRNOG00000021093
caenorhabditis_elegans		WBGENE00004912

Paralogs (3): SYNGR1 (ENSG00000100321), SYNGR2 (ENSG00000108639), SYNGR3 (ENSG00000127561)

Protein

Protein identifiers

Synaptogyrin-4 — O95473 (reviewed: O95473)

All UniProt accessions (5): O95473, A0A140VKF5, M0QXW6, M0QYL0, M0R1Y8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the synaptogyrin family.

RefSeq proteins (1): NP_036583* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008253	Marvel	Domain
IPR016579	Synaptogyrin	Family

Pfam: PF01284

UniProt features (8 total): transmembrane region 4, chain 1, domain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O95473-F1	77.93	0.41

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 104 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, E2F_Q4, MODULE_52, TGCGCANK_UNKNOWN, E2F4DP1_01, CHANDRAN_METASTASIS_DN, MODULE_118, NKX62_Q2, E2F1DP1_01, E2F1DP2_01, MODULE_88, E2F1_Q3, MODULE_18, HAMAI_APOPTOSIS_VIA_TRAIL_DN, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_4

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (3): synaptic vesicle membrane (GO:0030672), neuromuscular junction (GO:0031594), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
synaptic vesicle	1
exocytic vesicle membrane	1
synapse	1
cellular anatomical structure	1

Protein interactions and networks

STRING

507 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SYNGR4	PLEKHB1	Q9UF11	646
SYNGR4	TEX26	Q8N6G2	644
SYNGR4	FNDC8	Q8TC99	606
SYNGR4	ZNF681	Q96N22	471
SYNGR4	OR13J1	Q8NGT2	468
SYNGR4	DENND4A	Q7Z401	467
SYNGR4	PROSER2	Q86WR7	460
SYNGR4	THEM6	Q8WUY1	454
SYNGR4	TMEM220	Q6QAJ8	450
SYNGR4	TMEM143	Q96AN5	442
SYNGR4	SPACA4	Q8TDM5	441
SYNGR4	MXD3	Q9BW11	437
SYNGR4	SYP	P08247	397
SYNGR4	ANKRD29	Q8N6D5	376
SYNGR4	GLB1L	Q6UWU2	371

IntAct

2 interactions, top by confidence:

A	B	Type	Score
SYNGR4	GULP1	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (2): SYNGR4 (PCA), GULP1 (Affinity Capture-MS)

ESM2 similar proteins: A0A2R8RY99, A0PK11, A9UL59, B2RVW2, B4L184, B4LC58, B4N5D3, D3ZFW5, O95473, P23290, P35801, P35802, P35803, P36964, P36965, P51674, P56749, P58418, P79826, Q0IIL2, Q0P4G7, Q0VD07, Q11085, Q13491, Q2YDD6, Q53R12, Q5R603, Q5R9K1, Q5R9Q3, Q5R9R3, Q5T9L3, Q5ZLR1, Q6AYR5, Q6CRM6, Q6DID7, Q6P689, Q6UX40, Q754N9, Q7YWX7, Q812E9

Diamond homologs: A2VE58, A7E3W5, A8MWL6, O43759, O43760, O43761, O54980, O55100, O55101, O76735, O95473, Q2YDD6, Q5R703, Q62876, Q7JYV2, Q8R191, Q9Z1L2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

50 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	41
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

789 predictions. Top by Δscore:

Variant	Effect	Δscore
19:48365933:GGG:G	donor_gain	1.0000
19:48365934:GGG:G	donor_gain	1.0000
19:48373750:GGCTG:G	donor_gain	1.0000
19:48373751:GCTG:G	donor_gain	1.0000
19:48373751:GCTGG:G	donor_gain	1.0000
19:48373753:TGGT:T	donor_loss	1.0000
19:48373754:GGT:G	donor_loss	1.0000
19:48373755:G:GG	donor_gain	1.0000
19:48373755:GT:G	donor_loss	1.0000
19:48373756:T:A	donor_loss	1.0000
19:48375602:T:TA	acceptor_gain	1.0000
19:48373504:T:TA	acceptor_gain	0.9900
19:48373505:G:A	acceptor_gain	0.9900
19:48373511:CCACA:C	acceptor_loss	0.9900
19:48373512:CACAG:C	acceptor_loss	0.9900
19:48373513:ACAGG:A	acceptor_loss	0.9900
19:48373514:CA:C	acceptor_loss	0.9900
19:48373515:A:AG	acceptor_gain	0.9900
19:48373516:G:GG	acceptor_gain	0.9900
19:48373545:T:TA	acceptor_gain	0.9900
19:48373548:T:A	acceptor_gain	0.9900
19:48373753:TG:T	donor_gain	0.9900
19:48373754:GG:G	donor_gain	0.9900
19:48375600:T:A	acceptor_gain	0.9900
19:48375611:A:AG	acceptor_gain	0.9900
19:48375612:G:GG	acceptor_gain	0.9900
19:48365934:GG:G	donor_gain	0.9800
19:48365935:GG:G	donor_gain	0.9800
19:48373752:CTG:C	donor_gain	0.9800
19:48375612:GTT:G	acceptor_gain	0.9800

AlphaMissense

1544 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:48375642:T:C	F121L	0.920
19:48375644:C:A	F121L	0.920
19:48375644:C:G	F121L	0.920
19:48375726:T:C	F149L	0.884
19:48375728:C:A	F149L	0.884
19:48375728:C:G	F149L	0.884
19:48373535:T:C	F38L	0.879
19:48373537:C:A	F38L	0.879
19:48373537:C:G	F38L	0.879
19:48375630:T:A	W117R	0.875
19:48375630:T:C	W117R	0.875
19:48373670:T:C	F83L	0.868
19:48373672:C:A	F83L	0.868
19:48373672:C:G	F83L	0.868
19:48365894:T:C	F18L	0.850
19:48365896:T:A	F18L	0.850
19:48365896:T:G	F18L	0.850
19:48375618:T:A	W113R	0.845
19:48375618:T:C	W113R	0.845
19:48373658:A:C	S79R	0.840
19:48373660:C:A	S79R	0.840
19:48373660:C:G	S79R	0.840
19:48375750:T:A	W157R	0.832
19:48375750:T:C	W157R	0.832
19:48375665:G:C	W128C	0.824
19:48375665:G:T	W128C	0.824
19:48373520:T:C	F33L	0.794
19:48373522:C:A	F33L	0.794
19:48373522:C:G	F33L	0.794
19:48373592:T:A	C57S	0.785

dbSNP variants (sampled 300 via entrez): RS1000033332 (19:48364869 C>T), RS1000105781 (19:48373465 G>A), RS1000234394 (19:48370360 G>A), RS1000619979 (19:48369080 T>C), RS1000849988 (19:48367630 T>C), RS1000925104 (19:48367453 C>T), RS1001051116 (19:48369271 G>T), RS1001745581 (19:48363888 TCTCC>T), RS1002079296 (19:48362631 G>T), RS1002168962 (19:48366928 C>T), RS1002194103 (19:48373380 A>G), RS1002324348 (19:48368077 G>A), RS1002526276 (19:48371721 G>T), RS1002587692 (19:48366637 G>A), RS1002781124 (19:48372028 C>T)

Disease associations

OMIM: gene MIM:608373 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression	1
aflatoxin B2	decreases methylation	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	increases mutagenesis	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	decreases expression	1
Tamoxifen	increases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases methylation	1
Nanotubes, Carbon	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.