SYNDIG1

synapse differentiation inducing 1, the group of interferon induced transmembrane protein domain containing

Basic information

Region (hg38): 20:24469628-24666616

Previous symbols: [ "C20orf39", "TMEM90B" ]

Links

ENSG00000101463 ∙ NCBI:79953 ∙ OMIM:614311 ∙ HGNC:15885 ∙ Uniprot:Q9H7V2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SYNDIG1 gene.

• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNDIG1 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in SYNDIG1

This is a list of pathogenic ClinVar variants found in the SYNDIG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-24543103-T-G		not specified	Uncertain significance (Oct 03, 2022)
20-24543189-T-C		not specified	Uncertain significance (Feb 01, 2023)
20-24543303-C-T		not specified	Uncertain significance (Sep 15, 2021)
20-24543307-G-A		not specified	Uncertain significance (Jan 30, 2024)
20-24543323-C-G		not specified	Uncertain significance (Nov 17, 2022)
20-24543378-A-G		not specified	Uncertain significance (Mar 06, 2023)
20-24543413-G-A		not specified	Uncertain significance (Dec 18, 2023)
20-24584899-T-C		not specified	Uncertain significance (Mar 07, 2023)
20-24584911-G-A		not specified	Uncertain significance (Jun 22, 2023)
20-24584957-G-C		not specified	Uncertain significance (Jun 29, 2022)
20-24584970-G-A		not specified	Uncertain significance (Sep 17, 2021)
20-24665364-A-C		not specified	Uncertain significance (Dec 13, 2022)
20-24665434-T-C		not specified	Uncertain significance (Dec 15, 2023)
20-24665491-A-G		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNDIG1	protein_coding	protein_coding	ENST00000376862	3	197418

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.302	0.680	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.507	141	159	0.887	0.0000102	1696
Missense in Polyphen		42	55.2	0.76087		621
Synonymous	0.646	64	70.9	0.902	0.00000494	514
Loss of Function	2.01	2	8.20	0.244	3.55e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate AMPA receptor content at nascent synapses, and have a role in postsynaptic development and maturation. {ECO:0000250}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.31

Haploinsufficiency Scores

• pHI: 0.285
• hipred: Y
• hipred_score: 0.604
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syndig1

Gene ontology

• Biological process: intracellular protein transport;positive regulation of synapse assembly;synaptic vesicle clustering
• Cellular component: integral component of plasma membrane;postsynaptic density;cell junction;early endosome membrane;dendritic spine;dendritic shaft;intracellular membrane-bounded organelle;cell body;postsynaptic membrane;excitatory synapse;presynapse
• Molecular function: protein binding;glutamate receptor binding;protein homodimerization activity