SNTG1

syntrophin gamma 1, the group of PDZ domain containing

Basic information

Region (hg38): 8:49909789-50796692

Links

ENSG00000147481 ∙ NCBI:54212 ∙ OMIM:608714 ∙ HGNC:13740 ∙ Uniprot:Q9NSN8 ∙ 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 SNTG1 gene.

• not_specified (59 variants)
• SNTG1-related_disorder (16 variants)
• not_provided (6 variants)
• Gestational_diabetes_mellitus_uncontrolled (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNTG1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018967.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				7	1	8
missense			58	5	1	64
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	12	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNTG1	protein_coding	protein_coding	ENST00000522124	17	884330

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.163	0.837	125726	0	21	125747	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.329	289	274	1.06	0.0000140	3363
Missense in Polyphen		77	79.123	0.97317		971
Synonymous	-2.44	132	101	1.31	0.00000537	970
Loss of Function	3.98	8	32.5	0.246	0.00000155	388

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000908	0.0000905
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000114	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000100	0.0000967
Middle Eastern	0.000114	0.000109
South Asian	0.000177	0.000163
Other	0.00	0.00

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). May participate in regulating the subcellular location of diacylglycerol kinase-zeta to ensure that diacylglycerol is rapidly inactivated following receptor activation. {ECO:0000250}.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.639
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.74

Haploinsufficiency Scores

• pHI: 0.226
• hipred: Y
• hipred_score: 0.604
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.757

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sntg1

Gene ontology

• Biological process: cell communication
• Cellular component: nucleus;cytoplasm;cytoskeleton;dystrophin-associated glycoprotein complex;syntrophin complex;ruffle membrane
• Molecular function: actin binding;structural molecule activity;protein C-terminus binding