SNTG1

protein-coding

syntrophin gamma 1, the group of PDZ domain containing

Gene summary

The protein encoded by this gene is a member of the syntrophin family. Syntrophins are cytoplasmic peripheral membrane proteins that typically contain 2 pleckstrin homology (PH) domains, a PDZ domain that bisects the first PH domain, and a C-terminal domain that mediates dystrophin binding. This family member plays a role in mediating gamma-enolase trafficking to the plasma membrane and in enhancing its neurotrophic activity. Mutations in this gene are associated with idiopathic scoliosis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2016]

MANE transcript

NM_018967.5

Inheritance

—

ClinVar variants

U:80B:15

Top phenotype

SNTG1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr8:49,909,789-50,796,692

External References & Databases

Ensembl (ENSG00000147481)

Transcript & Mutation Effects

hg38 • Region Span ~886.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SNTG1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 71

SNTG1-related disorderTotal: 23

not providedTotal: 6

Gestational diabetes mellitus uncontrolledTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018967.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	8 clinvar	1 clinvar	10
missense			79 clinvar	5 clinvar	1 clinvar	85
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	80	13	2	95

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018967.5	RefSeq	NP_061840.1	17	MANE Select
ENST00000642720.2	Ensembl	ENSP00000493900.1	17	MANE Select
NM_001287813.3	RefSeq	NP_001274742.1	17	Standard
NM_001287814.3	RefSeq	NP_001274743.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell communication

Molecular Function

actin binding
structural molecule activity
protein C-terminus binding

Cellular Component

nucleus
cytoplasm
cytoskeleton
dystrophin-associated glycoprotein complex
syntrophin complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000522124
Coding exons: 17
Length: 884330
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 21
Defined: 125747
p: 0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.329	289	274	1.06	0.0000140	3363
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00010	0.000097	rare
South Asian	0.00018	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.757

Gene Damage Prediction

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