C9orf152

chromosome 9 open reading frame 152

Basic information

Region (hg38): 9:110190047-110208159

Links

ENSG00000188959 ∙ NCBI:401546 ∙ ∙ HGNC:31455 ∙ Uniprot:Q5JTZ5 ∙ 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 C9orf152 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C9orf152 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				1		1
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	1	0

Variants in C9orf152

This is a list of pathogenic ClinVar variants found in the C9orf152 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-110201438-T-C		not specified	Likely benign (Jul 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C9orf152	protein_coding	protein_coding	ENST00000400613	2	18142

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0179	0.902	121773	53	3917	125743	0.0159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.649	147	126	1.16	0.00000598	1539
Missense in Polyphen		38	27.402	1.3868		329
Synonymous	0.121	51	52.1	0.979	0.00000264	490
Loss of Function	1.48	4	8.71	0.459	4.54e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0115	0.0114
Ashkenazi Jewish	0.0197	0.0193
East Asian	0.000436	0.000435
Finnish	0.0102	0.0101
European (Non-Finnish)	0.0209	0.0209
Middle Eastern	0.000436	0.000435
South Asian	0.0263	0.0259
Other	0.0143	0.0143

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.0633
• hipred: N
• hipred_score: 0.123
• ghis: 0.413

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: D630039A03Rik