C9orf40

chromosome 9 open reading frame 40

Basic information

Region (hg38): 9:74946583-74952912

Links

ENSG00000135045 ∙ NCBI:55071 ∙ ∙ HGNC:23433 ∙ Uniprot:Q8IXQ3 ∙ 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 C9orf40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C9orf40 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
C9orf40	protein_coding	protein_coding	ENST00000376854	2	6306

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0697	0.752	125396	0	4	125400	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	58	83.9	0.692	0.00000380	1216
Missense in Polyphen		23	28.251	0.81413		327
Synonymous	1.41	24	34.5	0.696	0.00000157	405
Loss of Function	0.931	2	4.01	0.499	1.76e-7	55

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000913	0.0000913
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000885	0.00000884
Middle Eastern	0.00	0.00
South Asian	0.0000337	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.269
• hipred: N
• hipred_score: 0.204
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• 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: D030056L22Rik

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific