SIDT1

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

Basic information

Region (hg38): 3:113532554-113629575

Links

ENSG00000072858 ∙ NCBI:54847 ∙ OMIM:606816 ∙ HGNC:25967 ∙ Uniprot:Q9NXL6 ∙ 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 SIDT1 gene.

• Inborn genetic diseases (31 variants)
• Marfanoid habitus and intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIDT1 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			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	0

Variants in SIDT1

This is a list of pathogenic ClinVar variants found in the SIDT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-113533032-G-A		not specified	Uncertain significance (Jul 13, 2021)
3-113533052-T-C		not specified	Uncertain significance (Jul 19, 2022)
3-113533148-G-A		not specified	Uncertain significance (Oct 05, 2023)
3-113533202-G-C		not specified	Uncertain significance (Oct 12, 2021)
3-113566493-A-G		not specified	Uncertain significance (Dec 27, 2023)
3-113567554-A-G		not specified	Uncertain significance (Feb 03, 2022)
3-113567647-C-A		not specified	Uncertain significance (Jun 07, 2023)
3-113583427-G-A		not specified	Uncertain significance (Oct 27, 2022)
3-113583456-G-T		not specified	Uncertain significance (Apr 11, 2023)
3-113583473-G-A		not specified	Uncertain significance (Mar 02, 2023)
3-113584701-A-G		not specified	Uncertain significance (Nov 09, 2023)
3-113584713-C-G		not specified	Uncertain significance (Nov 12, 2021)
3-113584728-G-A		not specified	Uncertain significance (Feb 15, 2023)
3-113593028-G-T		not specified	Uncertain significance (Dec 20, 2023)
3-113593031-G-A		not specified	Uncertain significance (Aug 02, 2023)
3-113601633-C-A		not specified	Uncertain significance (Nov 13, 2023)
3-113603059-C-T		not specified	Uncertain significance (Sep 26, 2023)
3-113603072-C-A		not specified	Uncertain significance (Mar 13, 2023)
3-113603088-G-C		not specified	Uncertain significance (Jun 28, 2022)
3-113603143-G-T		not specified	Uncertain significance (Feb 13, 2024)
3-113603997-G-A		not specified	Uncertain significance (Feb 26, 2024)
3-113604915-T-C		not specified	Uncertain significance (Jul 12, 2022)
3-113607057-G-C		not specified	Uncertain significance (Feb 06, 2024)
3-113608135-T-C		not specified	Uncertain significance (Aug 02, 2023)
3-113608165-G-A		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIDT1	protein_coding	protein_coding	ENST00000264852	25	97283

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.51e-15	0.941	125509	2	237	125748	0.000951

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.110	480	473	1.01	0.0000261	5436
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00157	0.00157
Ashkenazi Jewish	0.00706	0.00677
East Asian	0.000627	0.000544
Finnish	0.0000939	0.0000924
European (Non-Finnish)	0.000564	0.000554
Middle Eastern	0.000627	0.000544
South Asian	0.00154	0.00154
Other	0.00137	0.00130

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.213
• hipred: N
• hipred_score: 0.408
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.413

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sidt1
• Phenotype: immune system phenotype

Gene ontology

• Biological process: dsRNA transport
• Cellular component: integral component of membrane
• Molecular function: RNA binding;RNA transmembrane transporter activity