SYNPO2L

synaptopodin 2 like, the group of PDZ domain containing

Basic information

Region (hg38): 10:73644881-73663803

Links

ENSG00000166317 ∙ NCBI:79933 ∙ ∙ HGNC:23532 ∙ Uniprot:Q9H987 ∙ 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 SYNPO2L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNPO2L 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			50			50
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	51	0	0

Variants in SYNPO2L

This is a list of pathogenic ClinVar variants found in the SYNPO2L region.

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

Position	Type	Phenotype	Significance	ClinVar
10-73646740-C-T		not specified	Uncertain significance (Aug 08, 2022)
10-73646774-C-T		not specified	Uncertain significance (May 03, 2023)
10-73646854-G-T		not specified	Uncertain significance (May 01, 2022)
10-73646939-T-C		not specified	Uncertain significance (Feb 27, 2023)
10-73647046-G-C		not specified	Uncertain significance (Jan 06, 2023)
10-73647053-C-T		not specified	Uncertain significance (Jul 20, 2021)
10-73647070-A-G		not specified	Uncertain significance (Jun 26, 2023)
10-73647175-C-G		not specified	Uncertain significance (Jun 13, 2024)
10-73647263-G-C		not specified	Uncertain significance (May 03, 2023)
10-73647263-G-T		not specified	Uncertain significance (Jun 28, 2023)
10-73647358-C-A		not specified	Uncertain significance (Oct 25, 2022)
10-73647454-C-T		not specified	Uncertain significance (Dec 27, 2023)
10-73647466-G-A		not specified	Uncertain significance (Aug 14, 2023)
10-73647503-T-C		not specified	Uncertain significance (Sep 06, 2022)
10-73647523-G-A		not specified	Uncertain significance (Feb 23, 2023)
10-73647531-A-AG			Uncertain significance (Mar 30, 2021)
10-73647533-G-A		not specified	Uncertain significance (Apr 18, 2023)
10-73647583-A-G		not specified	Uncertain significance (May 05, 2023)
10-73647658-G-A		not specified	Uncertain significance (Dec 20, 2021)
10-73647857-G-C		not specified	Uncertain significance (Apr 10, 2023)
10-73647884-G-A		not specified	Uncertain significance (Dec 11, 2023)
10-73647914-C-T		not specified	Uncertain significance (May 30, 2024)
10-73647926-T-C		not specified	Uncertain significance (Mar 28, 2023)
10-73647992-C-T		not specified	Uncertain significance (Sep 07, 2022)
10-73648081-C-T		not specified	Uncertain significance (Jun 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNPO2L	protein_coding	protein_coding	ENST00000394810	4	18923

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.75e-10	0.897	125368	0	377	125745	0.00150

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	474	562	0.843	0.0000312	6097
Missense in Polyphen		201	255.63	0.78628		2738
Synonymous	-0.0333	233	232	1.00	0.0000127	2303
Loss of Function	1.85	20	31.2	0.642	0.00000221	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00295	0.00293
Ashkenazi Jewish	0.00334	0.00288
East Asian	0.00294	0.00289
Finnish	0.000378	0.000323
European (Non-Finnish)	0.00129	0.00121
Middle Eastern	0.00294	0.00289
South Asian	0.00198	0.00183
Other	0.00156	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Actin-associated protein that may play a role in modulating actin-based shape. {ECO:0000250}.

Recessive Scores

• pRec: 0.0910

Intolerance Scores

• loftool: 0.794
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.7

Haploinsufficiency Scores

• pHI: 0.204
• hipred: N
• hipred_score: 0.497
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.218

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Synpo2l

Zebrafish Information Network

• Gene name: synpo2lb
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curved ventral

Gene ontology

• Biological process: heart morphogenesis;positive regulation of actin filament bundle assembly;positive regulation of Rho protein signal transduction;sarcomere organization;positive regulation of stress fiber assembly
• Cellular component: nucleus;nucleoplasm;cytosol;actin cytoskeleton;nuclear speck;Z disc;cell junction
• Molecular function: actin binding