SLX9

SLX9 ribosome biogenesis factor, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): 21:44940025-44976973

Previous symbols: [ "C21orf70", "FAM207A" ]

Links

ENSG00000160256 ∙ NCBI:85395 ∙ ∙ HGNC:15811 ∙ Uniprot:Q9NSI2 ∙ 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 SLX9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLX9 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			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	0

Variants in SLX9

This is a list of pathogenic ClinVar variants found in the SLX9 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-44940095-A-T		not specified	Uncertain significance (Sep 30, 2024)
21-44940113-A-G		not specified	Uncertain significance (Feb 12, 2024)
21-44940116-G-A		not specified	Uncertain significance (Jan 11, 2025)
21-44940145-G-A		not specified	Uncertain significance (Aug 21, 2023)
21-44940157-A-C		not specified	Uncertain significance (Nov 16, 2021)
21-44943690-G-A		not specified	Uncertain significance (Nov 18, 2022)
21-44943752-G-C		not specified	Uncertain significance (Oct 04, 2022)
21-44943765-G-A		not specified	Uncertain significance (Apr 07, 2022)
21-44943813-C-T		not specified	Uncertain significance (Jan 22, 2025)
21-44943814-G-A		not specified	Uncertain significance (Sep 26, 2024)
21-44960117-G-A		not specified	Likely benign (May 25, 2022)
21-44960130-A-G		not specified	Uncertain significance (Nov 22, 2021)
21-44960150-C-T		not specified	Uncertain significance (Aug 19, 2024)
21-44960151-G-A		not specified	Uncertain significance (Jan 24, 2024)
21-44967078-C-T		not specified	Uncertain significance (Aug 31, 2022)
21-44967094-C-T		not specified	Uncertain significance (Jun 22, 2021)
21-44967099-G-T		not specified	Uncertain significance (Nov 15, 2024)
21-44967138-G-A		not specified	Uncertain significance (Apr 26, 2023)
21-44967168-C-T		not specified	Uncertain significance (Jun 17, 2022)
21-44967177-C-T		not specified	Uncertain significance (Aug 12, 2021)
21-44967178-G-A		not specified	Likely benign (Jan 27, 2025)
21-44973201-G-A		not specified	Uncertain significance (Oct 26, 2021)
21-44973205-G-A		not specified	Uncertain significance (Mar 14, 2023)
21-44973207-A-G		not specified	Uncertain significance (Jan 17, 2025)
21-44973216-C-T		not specified	Uncertain significance (May 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLX9	protein_coding	protein_coding	ENST00000291634	6	36980

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0756	0.878	125712	0	33	125745	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0526	136	134	1.01	0.00000884	1445
Missense in Polyphen		43	42.649	1.0082		509
Synonymous	-0.164	57	55.4	1.03	0.00000351	486
Loss of Function	1.69	3	8.23	0.365	3.51e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000979	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.0000974	0.0000967
Middle Eastern	0.000979	0.000979
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0924

Intolerance Scores

• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.146
• ghis: 0.570

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam207a

Gene ontology

• Biological process: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• Cellular component: nucleolus;90S preribosome;preribosome, small subunit precursor
• Molecular function: protein binding