SYNDIG1

protein-coding

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

Gene summary

This gene encodes a protein that belongs to the interferon-induced transmembrane family of proteins. A similar protein in rat is thought to regulate the development of excitatory synapses. [provided by RefSeq, Jul 2013]

Previous symbols:

C20orf39
TMEM90B

MANE transcript

NM_024893.3

Inheritance

—

ClinVar variants

U:49

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr20:24,469,629-24,666,616

External References & Databases

Ensembl (ENSG00000101463)

Transcript & Mutation Effects

hg38 • Region Span ~197.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Tourette syndromeNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0007661

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SYNDIG1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024893.3. 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			1
missense			45 clinvar			45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	49	0	0	49

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 63 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024893.3	RefSeq	NP_079169.1	3	MANE Select
ENST00000376862.4	Ensembl	ENSP00000366058.3	3	MANE Select
NM_001323606.2	RefSeq	NP_001310535.1	3	Standard
NM_001323607.2	RefSeq	NP_001310536.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

intracellular protein transport
positive regulation of synapse assembly
synaptic vesicle clustering

Molecular Function

protein binding
glutamate receptor binding
protein homodimerization activity

Cellular Component

integral component of plasma membrane
postsynaptic density
cell junction
early endosome membrane
dendritic spine

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376862
Coding exons: 3
Length: 197418
Individuals with no LoFs: 125737
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125747
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.507	141	159	0.887	0.0000102	1696
Missense (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

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	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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