SNORD118

small nucleolar RNA, C/D box 118, the group of Small nucleolar RNAs, C/D box

Basic information

Region (hg38): 17:8173454-8173587

Links

ENSG00000200463 ∙ NCBI:727676 ∙ OMIM:616663 ∙ HGNC:32952 ∙ ∙ ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• leukoencephalopathy with calcifications and cysts (Strong), mode of inheritance: AR
• leukoencephalopathy with calcifications and cysts (Moderate), mode of inheritance: AR
• leukoencephalopathy with calcifications and cysts (Strong), mode of inheritance: AR
• leukoencephalopathy with calcifications and cysts (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Leukoencephalopathy, brain calcifications, and cysts (Labrune syndrome)	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Cardiovascular; Neurologic	27571260

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNORD118 gene.

• not provided (147 variants)
• Leukoencephalopathy with calcifications and cysts (41 variants)
• not specified (2 variants)
• TMEM107-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNORD118 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			2			2
splice region						0
non coding	19	3	106	21	18	167
Total	19	3	108	21	18

Highest pathogenic variant AF is 0.000131

Variants in SNORD118

This is a list of pathogenic ClinVar variants found in the SNORD118 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-8173455-T-C			Uncertain significance (Aug 01, 2023)
17-8173455-T-G			Uncertain significance (Apr 28, 2022)
17-8173456-C-CA			Uncertain significance (Nov 01, 2023)
17-8173458-G-C		Leukoencephalopathy with calcifications and cysts	Conflicting classifications of pathogenicity (Jan 02, 2024)
17-8173458-G-T		Leukoencephalopathy with calcifications and cysts	Pathogenic (Apr 06, 2020)
17-8173459-A-G		Leukoencephalopathy with calcifications and cysts	Pathogenic (Apr 06, 2020)
17-8173460-C-G			Uncertain significance (Dec 18, 2023)
17-8173460-C-T		TMEM107-related disorder	Benign (Jan 31, 2024)
17-8173460-CA-TG			Uncertain significance (Feb 14, 2022)
17-8173459-A-ATAGGAGCAATCAGGG			Uncertain significance (Mar 14, 2022)
17-8173462-G-C		Leukoencephalopathy with calcifications and cysts	Uncertain significance (Jan 11, 2024)
17-8173463-G-A		Leukoencephalopathy with calcifications and cysts	Uncertain significance (Aug 16, 2022)
17-8173465-G-A			Uncertain significance (Aug 16, 2022)
17-8173466-C-A			Uncertain significance (Oct 24, 2022)
17-8173466-C-G			Uncertain significance (Jul 21, 2023)
17-8173466-C-T			Uncertain significance (Sep 07, 2022)
17-8173469-T-C			Uncertain significance (Aug 15, 2022)
17-8173470-C-A		Leukoencephalopathy with calcifications and cysts	Uncertain significance (Sep 17, 2019)
17-8173470-C-G			Uncertain significance (May 22, 2023)
17-8173472-G-A			Uncertain significance (Aug 09, 2022)
17-8173473-G-A			Benign/Likely benign (Jul 01, 2024)
17-8173473-G-C			Uncertain significance (Dec 26, 2023)
17-8173474-G-A			Uncertain significance (Jan 22, 2024)
17-8173475-T-A			Uncertain significance (Oct 17, 2022)
17-8173475-T-G			Uncertain significance (Mar 14, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP