SNPH

syntaphilin

Basic information

Region (hg38): 20:1266280-1309328

Links

ENSG00000101298 ∙ NCBI:9751 ∙ OMIM:604942 ∙ HGNC:15931 ∙ Uniprot:O15079 ∙ 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 SNPH gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNPH 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in SNPH

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

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

Position	Type	Phenotype	Significance	ClinVar
20-1297246-C-T		not specified	Uncertain significance (Feb 13, 2024)
20-1300579-C-T		not specified	Uncertain significance (May 29, 2024)
20-1300587-A-T		not specified	Uncertain significance (Nov 08, 2022)
20-1300697-C-A		not specified	Uncertain significance (Feb 13, 2023)
20-1305017-G-C		not specified	Uncertain significance (Sep 29, 2023)
20-1305044-A-C		not specified	Uncertain significance (Sep 22, 2022)
20-1305047-G-A		not specified	Uncertain significance (Sep 28, 2022)
20-1305281-G-A		not specified	Uncertain significance (Jul 25, 2023)
20-1305317-G-A		not specified	Uncertain significance (Dec 01, 2022)
20-1305360-T-C		not specified	Uncertain significance (Feb 06, 2023)
20-1305444-C-A		not specified	Uncertain significance (Feb 27, 2023)
20-1305494-A-T		not specified	Uncertain significance (Jul 27, 2021)
20-1305503-C-T		not specified	Uncertain significance (Aug 19, 2023)
20-1305612-G-A		not specified	Uncertain significance (Sep 06, 2022)
20-1305728-C-T		not specified	Uncertain significance (Feb 14, 2023)
20-1305759-C-T		not specified	Uncertain significance (Aug 02, 2022)
20-1305823-G-C		not specified	Uncertain significance (Aug 17, 2022)
20-1305885-C-T		not specified	Uncertain significance (Oct 03, 2022)
20-1305903-G-A		not specified	Uncertain significance (Jun 19, 2024)
20-1306028-C-A		not specified	Uncertain significance (Jun 29, 2022)
20-1306037-G-A		not specified	Uncertain significance (Aug 22, 2023)
20-1306041-G-A		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNPH	protein_coding	protein_coding	ENST00000381873	4	43013

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.971	0.0292	125719	0	3	125722	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	232	306	0.758	0.0000197	3179
Missense in Polyphen		90	130.57	0.68926		1345
Synonymous	0.237	129	132	0.974	0.00000848	1035
Loss of Function	3.39	1	15.3	0.0652	7.38e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits SNARE complex formation by absorbing free syntaxin-1. {ECO:0000269|PubMed:10707983}.

Intolerance Scores

• loftool: 0.0116
• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.53

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.786
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.128

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snph
• Phenotype: cellular 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: neurotransmitter secretion;brain development;synaptic vesicle docking;neuron differentiation
• Cellular component: cytoplasm;cytoplasmic microtubule;integral component of membrane;cell junction;mitochondrial membrane;presynaptic membrane;neuron projection;neuronal cell body
• Molecular function: syntaxin-1 binding