CMSS1

protein-coding

cms1 ribosomal small subunit homolog

Gene summary

Enables RNA binding activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C3orf26

MANE transcript

NM_032359.4

Inheritance

—

ClinVar variants

U:38B:1

Top phenotype

FILIP1L-related disorder

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr3:99,817,837-100,181,732

External References & Databases

Ensembl (ENSG00000184220)

Transcript & Mutation Effects

hg38 • Region Span ~363.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CMSS1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 231

FILIP1L-related disorderTotal: 17

not providedTotal: 1

CMSS1-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032359.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			36 clinvar	1 clinvar		37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	38	1	0	39

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032359.4	RefSeq	NP_115735.2	10	MANE Select
ENST00000421999.8	Ensembl	ENSP00000410396.2	10	MANE Select
NM_001167924.2	RefSeq	NP_001161396.1	10	Standard
ENST00000463526.1	Ensembl	ENSP00000418855.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000421999
Coding exons: 10
Length: 360770
Individuals with no LoFs: 125723
Homozygous LoFs: 1
Heterozygous LoFs: 24
Defined: 125748
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.358	157	145	1.08	0.00000719	1817
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.00023	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0967

Intolerance Scores

RVIS EVS: 0.24
RVIS percentile EVS: 68.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N

Gene Damage Prediction

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