SNTG2

syntrophin gamma 2, the group of PDZ domain containing

Basic information

Region (hg38): 2:950849-1367613

Links

ENSG00000172554 ∙ NCBI:54221 ∙ OMIM:608715 ∙ HGNC:13741 ∙ Uniprot:Q9NY99 ∙ 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 SNTG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNTG2 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				6	5	11
missense			42	5	2	49
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	11	7

Variants in SNTG2

This is a list of pathogenic ClinVar variants found in the SNTG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-951013-C-T		not specified	Uncertain significance (Feb 28, 2024)
2-951027-G-A		not specified	Uncertain significance (May 13, 2024)
2-951039-C-G		not specified	Uncertain significance (Nov 01, 2022)
2-1083536-C-A		not specified	Uncertain significance (Oct 04, 2022)
2-1083548-G-A		not specified	Uncertain significance (Aug 04, 2023)
2-1083555-C-A		not specified	Uncertain significance (Aug 30, 2022)
2-1083557-G-A		not specified	Uncertain significance (May 14, 2024)
2-1083569-G-A		not specified	Uncertain significance (Jan 22, 2024)
2-1083573-T-C		not specified	Uncertain significance (Dec 28, 2022)
2-1083588-C-T			Likely benign (Dec 31, 2019)
2-1083594-A-C			Benign (Aug 15, 2018)
2-1083616-A-G			Benign (Jun 13, 2018)
2-1083646-G-C		not specified	Likely benign (Jul 06, 2021)
2-1083648-G-A		not specified	Uncertain significance (Apr 20, 2023)
2-1098196-C-T		not specified	Uncertain significance (Apr 06, 2023)
2-1098202-A-G		not specified	Uncertain significance (Aug 16, 2022)
2-1098209-C-A		not specified	Uncertain significance (May 26, 2022)
2-1137645-G-T		not specified	Uncertain significance (Dec 20, 2023)
2-1137782-T-G		not specified	Uncertain significance (Mar 01, 2023)
2-1165604-G-A			Benign (Dec 31, 2019)
2-1165612-C-T		not specified	Uncertain significance (Feb 01, 2023)
2-1165613-G-A			Likely benign (Dec 31, 2019)
2-1165630-C-T		not specified	Uncertain significance (May 20, 2024)
2-1173108-C-T			Benign (Dec 31, 2019)
2-1173125-G-C		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNTG2	protein_coding	protein_coding	ENST00000308624	17	424832

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.31e-14	0.159	124546	0	133	124679	0.000534

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.190	317	308	1.03	0.0000180	3508
Missense in Polyphen		87	90.318	0.96326		1063
Synonymous	0.206	129	132	0.977	0.00000935	1028
Loss of Function	1.03	25	31.2	0.801	0.00000154	366

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00360	0.00359
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000111
Finnish	0.000235	0.000232
European (Non-Finnish)	0.000455	0.000451
Middle Eastern	0.000113	0.000111
South Asian	0.000463	0.000458
Other	0.000333	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein that binds to and probably organizes the subcellular localization of a variety of proteins. May link various receptors to the actin cytoskeleton and the dystrophin glycoprotein complex (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.913
• rvis_EVS: 1
• rvis_percentile_EVS: 90.77

Haploinsufficiency Scores

• pHI: 0.160
• hipred: N
• hipred_score: 0.301
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0484

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sntg2

Gene ontology

• Biological process: central nervous system development
• Cellular component: cytoplasm;cytoskeleton;dystrophin-associated glycoprotein complex;syntrophin complex;sarcolemma
• Molecular function: actin binding;structural molecule activity;PDZ domain binding;neuroligin family protein binding