SIDT2

SID1 transmembrane family member 2

Basic information

Region (hg38): 11:117178735-117197445

Links

ENSG00000149577 ∙ NCBI:51092 ∙ OMIM:617551 ∙ HGNC:24272 ∙ Uniprot:Q8NBJ9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SIDT2 gene.

• Inborn genetic diseases (26 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIDT2 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				2	1	3
missense			24	1	1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	24	3	2

Variants in SIDT2

This is a list of pathogenic ClinVar variants found in the SIDT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-117179401-G-C		not specified	Uncertain significance (Jun 16, 2023)
11-117181421-G-C		not specified	Uncertain significance (Jun 24, 2022)
11-117181465-C-T		not specified	Uncertain significance (Jun 09, 2022)
11-117181488-C-A		not specified	Uncertain significance (Feb 23, 2023)
11-117181807-G-A		not specified	Uncertain significance (Feb 22, 2023)
11-117181859-C-T		not specified	Uncertain significance (Dec 02, 2022)
11-117181893-A-C		not specified	Uncertain significance (Oct 17, 2023)
11-117181895-G-A		not specified	Uncertain significance (Sep 27, 2022)
11-117181952-A-G		not specified	Uncertain significance (Apr 17, 2023)
11-117181958-G-A		not specified	Uncertain significance (Aug 02, 2021)
11-117182526-A-C		not specified	Uncertain significance (Apr 07, 2022)
11-117182567-G-A		not specified	Uncertain significance (Oct 26, 2022)
11-117182726-C-G		not specified	Uncertain significance (Jul 25, 2023)
11-117182742-A-G		not specified	Uncertain significance (Jan 11, 2023)
11-117182750-G-A		not specified	Uncertain significance (May 09, 2023)
11-117183779-C-T		not specified	Uncertain significance (Dec 13, 2022)
11-117183860-T-G		not specified	Uncertain significance (Jan 02, 2024)
11-117186578-A-G			Benign (Jan 31, 2018)
11-117186613-T-C		not specified	Uncertain significance (Jan 10, 2022)
11-117187382-C-A		not specified	Uncertain significance (Nov 17, 2022)
11-117187648-G-A		not specified	Uncertain significance (Apr 12, 2023)
11-117187689-C-T			Likely benign (Jan 01, 2023)
11-117188710-C-T		not specified	Uncertain significance (May 03, 2023)
11-117188711-G-A		not specified	Uncertain significance (Nov 27, 2023)
11-117188731-A-G		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIDT2	protein_coding	protein_coding	ENST00000324225	26	18712

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.20e-10	1.00	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	389	513	0.758	0.0000316	5446
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000904	0.000904
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000109	0.000109
South Asian	0.000294	0.000294
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.458
• hipred: Y
• hipred_score: 0.563
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.569

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sidt2
• Phenotype: immune system phenotype; liver/biliary system phenotype; normal phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: cell morphogenesis;type B pancreatic cell development;RNA catabolic process;response to glucose;dsRNA transport;glucose homeostasis;type B pancreatic cell proliferation;RNA transport;regulation of insulin secretion involved in cellular response to glucose stimulus
• Cellular component: lysosome;lysosomal membrane;plasma membrane;integral component of membrane
• Molecular function: DNA binding;double-stranded RNA binding;AP-2 adaptor complex binding;AP-1 adaptor complex binding;nucleic acid transmembrane transporter activity;RNA transmembrane transporter activity