C9orf78

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

Basic information

Region (hg38): 9:129827290-129835863

Links

ENSG00000136819

∙ NCBI:51759 ∙ OMIM:619569 ∙ HGNC:24932 ∙ Uniprot:Q9NZ63 ∙ 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 C9orf78 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C9orf78 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)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C9orf78	protein_coding	protein_coding	ENST00000372447	9	8574

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000192	0.900	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	105	172	0.610	0.00000969	1918
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

pRec: 0.113

Intolerance Scores

loftool: 0.635
rvis_EVS: -0.14
rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

pHI: 0.164
hipred: Y
hipred_score: 0.532
ghis: 0.508

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: BC005624
Phenotype

Gene ontology

Biological process: regulation of mRNA splicing, via spliceosome
Cellular component: nucleus;nucleoplasm;spliceosomal complex;cytosol
Molecular function: protein binding