SIDT1

protein-coding

SID1 transmembrane family member 1, the group of MicroRNA protein coding host genes

Gene summary

The protein encoded by this gene belongs to SID1 family of transmembrane dsRNA-gated channels. Family members transport dsRNA into cells and are required for systemic RNA interference. [provided by RefSeq, May 2017]

MANE transcript

NM_017699.3

Inheritance

—

ClinVar variants

U:133B:2

Top phenotype

Marfanoid habitus and intellectual disability

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr3:113,532,555-113,629,714

External References & Databases

Ensembl (ENSG00000072858)

Transcript & Mutation Effects

hg38 • Region Span ~97.2 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 SIDT1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 124

Marfanoid habitus and intellectual disabilityTotal: 1

Long QT syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017699.3. 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			127 clinvar	2 clinvar		129
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	133	2	0	135

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017699.3	RefSeq	NP_060169.2	25	MANE Select
ENST00000264852.9	Ensembl	ENSP00000264852.4	25	MANE Select
NM_001308350.2	RefSeq	NP_001295279.1	26	Standard
NM_001322294.2	RefSeq	NP_001309223.1	26	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

dsRNA transport

Molecular Function

RNA binding
RNA transmembrane transporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000264852
Coding exons: 25
Length: 97283
Individuals with no LoFs: 125509
Homozygous LoFs: 2
Heterozygous LoFs: 237
Defined: 125748
p: 0.000951

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.110	480	473	1.01	0.0000261	5436
Missense (PolyPhen)		187	181.52	1.0302		2067
Synonymous	0.412	177	184	0.961	0.0000108	1575
Loss of Function	2.26	30	46.7	0.643	0.00000215	554

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00056	0.00055	rare
Latino/Admixed American	0.0010	0.00093	notable
Ashkenazi Jewish	0.0071	0.0068	notable
East Asian	0.00063	0.00054	rare
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.00056	0.00055	rare
South Asian	0.0015	0.0015	notable
Other	0.0014	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: In vitro binds long double-stranded RNA (dsRNA) (500 and 700 base pairs), but not dsRNA shorter than 300 bp. Not involved in RNA autophagy, a process in which RNA is directly imported into lysosomes in an ATP-dependent manner, and degraded. {ECO:0000250|UniProtKB:Q6AXF6}.;

Recessive Scores

pRec: 0.120

Intolerance Scores

LoFtool: 0.982
RVIS EVS: -0.92
RVIS percentile EVS: 9.78

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.413

Gene Damage Prediction

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