CMSS1

cms1 ribosomal small subunit homolog

Basic information

Region (hg38): 3:99817837-100181732

Previous symbols: [ "C3orf26" ]

Links

ENSG00000184220 ∙ NCBI:84319 ∙ ∙ HGNC:28666 ∙ Uniprot:Q9BQ75 ∙ 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 CMSS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMSS1 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			79	11	9	99
Total	0	0	94	11	9

Variants in CMSS1

This is a list of pathogenic ClinVar variants found in the CMSS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-99818001-G-C		not specified	Uncertain significance (Aug 01, 2022)
3-99818026-G-A		not specified	Uncertain significance (Oct 13, 2023)
3-99833233-G-A		FILIP1L-related disorder	Likely benign (Sep 05, 2019)
3-99848311-C-T		not specified	Uncertain significance (Jun 17, 2024)
3-99848393-A-G		FILIP1L-related disorder	Likely benign (Apr 24, 2019)
3-99848431-C-T		FILIP1L-related disorder	Benign (Jan 02, 2020)
3-99848465-T-A		not specified	Uncertain significance (Dec 18, 2023)
3-99848539-C-T		not specified	Uncertain significance (Oct 12, 2022)
3-99848552-A-G		not specified	Uncertain significance (May 09, 2023)
3-99848558-A-C		not specified	Uncertain significance (Feb 23, 2023)
3-99848737-G-C		not specified	Uncertain significance (Feb 26, 2024)
3-99848755-G-A		not specified	Uncertain significance (Feb 14, 2023)
3-99848762-C-T		not specified	Uncertain significance (Feb 07, 2023)
3-99848767-T-C		not specified	Uncertain significance (Nov 03, 2022)
3-99848776-A-G		not specified	Uncertain significance (Oct 04, 2022)
3-99848777-T-G		not specified	Uncertain significance (Aug 09, 2021)
3-99848807-C-A		not specified	Uncertain significance (Sep 20, 2023)
3-99848842-C-T		not specified	Uncertain significance (Jun 12, 2023)
3-99848854-G-A		not specified	Uncertain significance (Nov 03, 2022)
3-99848865-C-G		FILIP1L-related disorder	Likely benign (Jul 16, 2019)
3-99848880-A-G		FILIP1L-related disorder	Likely benign (Aug 27, 2019)
3-99848960-C-A		not specified	Uncertain significance (Jun 24, 2022)
3-99848983-G-C		not specified	Uncertain significance (Jan 31, 2023)
3-99848984-G-A		not specified	Uncertain significance (Jan 31, 2023)
3-99849016-A-G		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMSS1	protein_coding	protein_coding	ENST00000421999	10	360770

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00112	0.990	125723	1	24	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.358	157	145	1.08	0.00000719	1817
Missense in Polyphen		25	35.532	0.70359		462
Synonymous	0.827	48	55.9	0.859	0.00000319	503
Loss of Function	2.29	8	18.7	0.428	8.76e-7	236

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000364	0.000363
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.000327	0.000326
South Asian	0.000229	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0967

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• pHI: 0.0875
• hipred: N
• hipred_score: 0.303
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cmss1

Gene ontology

• Molecular function: RNA binding