C9orf78

protein-coding

chromosome 9 open reading frame 78, the group of Spliceosomal P complex

Gene summary

Enables U5 snRNA binding activity. Involved in mRNA cis splicing, via spliceosome and regulation of homologous chromosome segregation. Located in chromosome, centromeric region and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_016520.3

Inheritance

—

ClinVar variants

U:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr9:129,827,290-129,835,863

External References & Databases

Ensembl (ENSG00000136819)

Transcript & Mutation Effects

hg38 • Region Span ~8.6 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 C9orf78 variants in ClinVar

0 Conditions Cataloged

No annotated ClinVar phenotypes.

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016520.3. 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			2 clinvar			2
missense						0
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	8	0	0	8

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 46 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016520.3	RefSeq	NP_057604.1	9	MANE Select
ENST00000372447.7	Ensembl	ENSP00000361524.3	9	MANE Select
ENST00000875653.1	Ensembl	ENSP00000545712.1	10	Standard
ENST00000875653.2	Ensembl	ENSP00000545712.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Biological Process

regulation of mRNA splicing, via spliceosome

Molecular Function

protein binding

Cellular Component

nucleus
nucleoplasm
spliceosomal complex
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372447
Coding exons: 9
Length: 8574
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125748
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.82	105	172	0.610	0.00000969	1918
Missense (PolyPhen)		10	41.364	0.24176		513
Synonymous	-0.251	65	62.5	1.04	0.00000359	514
Loss of Function	1.55	10	16.9	0.592	9.00e-7	202

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00016	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the regulation of telomeric heterochromatin assembly and control of telomere length. {ECO:0000250|UniProtKB:Q10148}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.635
RVIS EVS: -0.14
RVIS percentile EVS: 42.88

Essentials

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

Gene Damage Prediction

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