SIDT2

protein-coding

SID1 transmembrane family member 2

Gene summary

Predicted to enable several functions, including AP-1 adaptor complex binding activity; AP-2 adaptor complex binding activity; and RNA transmembrane transporter activity. Involved in RNA transport. Located in lysosomal membrane and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001040455.2

Inheritance

—

ClinVar variants

U:114B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr11:117,178,736-117,197,445

External References & Databases

Ensembl (ENSG00000149577)

Transcript & Mutation Effects

hg38 • Region Span ~18.7 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 SIDT2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 107

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001040455.2. 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			2 clinvar	3 clinvar	1 clinvar	6
missense			109 clinvar	1 clinvar	1 clinvar	111
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	114	4	2	120

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001040455.2	RefSeq	NP_001035545.1	26	MANE Select
ENST00000324225.9	Ensembl	ENSP00000314023.4	26	MANE Select
ENST00000278951.11	Ensembl	ENSP00000278951.7	26	Standard
ENST00000278951.12	Ensembl	ENSP00000278951.7	26	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell morphogenesis
type B pancreatic cell development
RNA catabolic process
response to glucose
dsRNA transport

Molecular Function

DNA binding
double-stranded RNA binding
AP-2 adaptor complex binding
AP-1 adaptor complex binding
nucleic acid transmembrane transporter activity

Cellular Component

lysosome
lysosomal membrane
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000324225
Coding exons: 26
Length: 18712
Individuals with no LoFs: 125685
Homozygous LoFs: 0
Heterozygous LoFs: 63
Defined: 125748
p: 0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.95	389	513	0.758	0.0000316	5446
Missense (PolyPhen)		133	234.07	0.5682		2516
Synonymous	-1.50	243	215	1.13	0.0000141	1632
Loss of Function	3.50	25	52.3	0.478	0.00000262	550

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00078	0.00078	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.00029	0.00029	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mediates the translocation of RNA and DNA across the lysosomal membrane during RNA and DNA autophagy (RDA), a process in which RNA or DNA is directly imported into lysosomes in an ATP- dependent manner, and degraded (PubMed:27046251, PubMed:27846365). Involved in the uptake of single-stranded oligonucleotides by living cells, a process called gymnosis (PubMed:28277980). Involved in the uptake of single-stranded oligonucleotides by living cells, a process called gymnosis. In vitro, mediates the uptake of linear DNA more efficiently than that of circular DNA, but exhibits similar uptake efficacy toward RNA and DNA. Binds long double-stranded RNA (dsRNA) (500 - 700 base pairs), but not dsRNA shorter than 100 bp (By similarity). {ECO:0000250|UniProtKB:Q8CIF6, ECO:0000269|PubMed:27046251, ECO:0000269|PubMed:27846365, ECO:0000269|PubMed:28277980}.;

Intolerance Scores

LoFtool: 0.678
RVIS EVS: -0.04
RVIS percentile EVS: 50.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.569

Gene Damage Prediction

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