SNHG28

small nucleolar RNA host gene 28, the group of Small nucleolar RNA non-coding host genes

Basic information

Region (hg38): 1:159834480-159855071

Previous symbols: [ "C1orf204" ]

Links

ENSG00000188004 ∙ NCBI:284677 ∙ ∙ HGNC:27647 ∙ Uniprot:P0DPA3 ∙ 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 SNHG28 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNHG28 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)			1			1
splice region						0
non coding			5			5
Total	0	0	6	0	0

Variants in SNHG28

This is a list of pathogenic ClinVar variants found in the SNHG28 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-159840864-C-T		not specified	Likely benign (Jul 21, 2021)
1-159841214-C-G		not specified	Uncertain significance (Jun 22, 2021)
1-159854838-G-A		not specified	Uncertain significance (Apr 11, 2023)
1-159854860-C-T		not specified	Uncertain significance (Jan 31, 2022)
1-159854898-C-T		not specified	Uncertain significance (Mar 19, 2024)
1-159854907-G-C		not specified	Uncertain significance (Nov 03, 2022)
1-159854920-A-T		not specified	Uncertain significance (Mar 21, 2023)
1-159854925-C-A		not specified	Uncertain significance (Dec 03, 2021)
1-159854956-G-A		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNHG28	protein_coding	protein_coding	ENST00000368102	5	20874

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.30e-8	0.0587	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.592	91	108	0.840	0.00000494	1467
Missense in Polyphen		17	16.228	1.0476		242
Synonymous	0.806	37	43.8	0.845	0.00000208	484
Loss of Function	-0.593	11	9.07	1.21	3.90e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0940

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_gene_trap: N

Gene ontology

• Molecular function: RNA binding