SYNPO

synaptopodin

Basic information

Region (hg38): 5:150601080-150659207

Links

ENSG00000171992 ∙ NCBI:11346 ∙ OMIM:608155 ∙ HGNC:30672 ∙ Uniprot:Q8N3V7 ∙ 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 SYNPO gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNPO 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				34	7	41
missense			114	9	5	128
nonsense						0
start loss						0
frameshift			1			1
inframe indel			13			13
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding			2	1	6	9
Total	0	0	130	44	18

Variants in SYNPO

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

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

Position	Type	Phenotype	Significance	ClinVar
5-150617912-G-A			Benign (May 17, 2021)
5-150617974-T-C			Benign (May 17, 2021)
5-150618097-C-A			Benign (May 17, 2021)
5-150618349-G-A			Benign (May 17, 2021)
5-150618484-G-T		not specified	Uncertain significance (Sep 01, 2021)
5-150618566-G-A			Benign (May 17, 2021)
5-150618595-AC-A		SYNPO-related disorder	Uncertain significance (Aug 19, 2023)
5-150618756-C-T			Likely benign (Oct 01, 2023)
5-150647992-A-C		not specified	Uncertain significance (Jan 19, 2024)
5-150648019-A-G		not specified	Uncertain significance (Dec 09, 2023)
5-150648025-C-T		not specified	Uncertain significance (Dec 19, 2022)
5-150648043-A-G		not specified	Uncertain significance (Dec 21, 2022)
5-150648049-G-A		not specified	Uncertain significance (Aug 17, 2022)
5-150648148-G-C		not specified	Uncertain significance (May 26, 2023)
5-150648205-C-T		not specified	Uncertain significance (Apr 05, 2023)
5-150648287-C-T			Likely benign (Dec 12, 2023)
5-150648290-A-G			Likely benign (Mar 04, 2022)
5-150648310-G-A		not specified	Uncertain significance (Apr 12, 2024)
5-150648418-G-A		not specified	Uncertain significance (Jun 11, 2021)
5-150648438-C-T			Uncertain significance (Aug 23, 2022)
5-150648447-C-T		not specified	Uncertain significance (Sep 17, 2023)
5-150648494-T-A			Likely benign (Jun 29, 2018)
5-150648499-C-T		not specified	Uncertain significance (Oct 14, 2023)
5-150648512-G-A			Likely benign (Dec 06, 2022)
5-150648547-C-T		not specified	Conflicting classifications of pathogenicity (Oct 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNPO	protein_coding	protein_coding	ENST00000394243	2	58141

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.986	0.0143	125038	0	3	125041	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.934	496	558	0.889	0.0000361	5930
Missense in Polyphen		174	226.14	0.76943		2400
Synonymous	0.501	238	248	0.960	0.0000174	2078
Loss of Function	4.19	3	26.1	0.115	0.00000169	276

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000630	0.0000617
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Actin-associated protein that may play a role in modulating actin-based shape and motility of dendritic spines and renal podocyte foot processes. Seems to be essential for the formation of spine apparatuses in spines of telencephalic neurons, which is involved in synaptic plasticity (By similarity). {ECO:0000250}.
• Pathway: Tight junction - Homo sapiens (human);Primary Focal Segmental Glomerulosclerosis FSGS (Consensus)

Recessive Scores

• pRec: 0.165

Intolerance Scores

• loftool: 0.0129
• rvis_EVS: -0.17
• rvis_percentile_EVS: 40.68

Haploinsufficiency Scores

• pHI: 0.427
• hipred: N
• hipred_score: 0.458
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.811

Gene Damage Prediction

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

Mouse Genome Informatics

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

Gene ontology

• Biological process: visual learning;positive regulation of actin filament bundle assembly;regulation of long-term neuronal synaptic plasticity;modification of dendritic spine;postsynaptic modulation of chemical synaptic transmission;positive regulation of postsynaptic cytosolic calcium concentration;spine apparatus assembly
• Cellular component: stress fiber;nucleus;bicellular tight junction;postsynaptic density;actin cytoskeleton;Z disc;dendritic spine;perikaryon;postsynaptic membrane;spine apparatus;Schaffer collateral - CA1 synapse;glutamatergic synapse
• Molecular function: actin binding;protein binding