SNTG2

protein-coding

syntrophin gamma 2, the group of PDZ domain containing

Gene summary

This gene encodes a protein belonging to the syntrophin family. Syntrophins are cytoplasmic peripheral membrane proteins that bind to components of mechanosenstive sodium channels and the extreme carboxy-terminal domain of dystrophin and dystrophin-related proteins. The PDZ domain of this protein product interacts with a protein component of a mechanosensitive sodium channel that affects channel gating. Absence or reduction of this protein product has been associated with Duchenne muscular dystrophy. There is evidence of alternative splicing yet the full-length nature of these variants has not been described. [provided by RefSeq, Jul 2008]

MANE transcript

NM_018968.4

Inheritance

—

ClinVar variants

U:98B:25

Top phenotype

High myopia

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr2:950,849-1,367,613

External References & Databases

Ensembl (ENSG00000172554)

Transcript & Mutation Effects

hg38 • Region Span ~416.8 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 SNTG2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 104

not providedTotal: 19

High myopiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018968.4. 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				7 clinvar	5 clinvar	12
missense			96 clinvar	12 clinvar	1 clinvar	109
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	98	19	6	123

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018968.4	RefSeq	NP_061841.2	17	MANE Select
ENST00000308624.10	Ensembl	ENSP00000311837.5	17	MANE Select
ENST00000407292.1	Ensembl	ENSP00000385020.1	11	Standard
ENST00000407292.2	Ensembl	ENSP00000385020.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

central nervous system development

Molecular Function

actin binding
structural molecule activity
PDZ domain binding
neuroligin family protein binding

Cellular Component

cytoplasm
cytoskeleton
dystrophin-associated glycoprotein complex
syntrophin complex
sarcolemma

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000308624
Coding exons: 17
Length: 424832
Individuals with no LoFs: 124546
Homozygous LoFs: 0
Heterozygous LoFs: 133
Defined: 124679
p: 0.000534

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.190	317	308	1.03	0.0000180	3508
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0034	0.0034	notable
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.00045	0.00045	rare
South Asian	0.00046	0.00046	rare
Other	0.00033	0.00033	rare

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). {ECO:0000250}.;

Recessive Scores

pRec: 0.144

Intolerance Scores

LoFtool: 0.913
RVIS EVS: 1
RVIS percentile EVS: 90.77

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0484

Gene Damage Prediction

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