C9orf24

chromosome 9 open reading frame 24

Basic information

Region (hg38): 9:34379018-34397828

Links

ENSG00000164972 ∙ NCBI:84688 ∙ OMIM:619502 ∙ HGNC:19919 ∙ Uniprot:Q8NCR6 ∙ 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 C9orf24 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C9orf24 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			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	0

Variants in C9orf24

This is a list of pathogenic ClinVar variants found in the C9orf24 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-34379651-G-T		not specified	Uncertain significance (Jul 14, 2021)
9-34380916-G-C		not specified	Uncertain significance (Oct 29, 2021)
9-34381083-T-G		not specified	Likely benign (Oct 29, 2021)
9-34382773-T-A		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C9orf24	protein_coding	protein_coding	ENST00000297623	6	18814

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000214	0.722	125684	0	64	125748	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.429	168	153	1.10	0.00000724	1671
Missense in Polyphen		73	68.64	1.0635		772
Synonymous	0.765	54	61.6	0.876	0.00000285	521
Loss of Function	1.16	11	16.0	0.687	8.24e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00113	0.00111
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000574	0.0000544
Finnish	0.000509	0.000508
European (Non-Finnish)	0.000170	0.000167
Middle Eastern	0.0000574	0.0000544
South Asian	0.000229	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in spermatogenesis (By similarity). May be involved in differentiation or function of ciliated cells. {ECO:0000250, ECO:0000269|PubMed:15242845}.

Recessive Scores

• pRec: 0.0931

Intolerance Scores

• loftool: 0.619
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.144
• ghis: 0.460

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: 1110017D15Rik
• Phenotype: normal phenotype