C9orf50

chromosome 9 open reading frame 50

Basic information

Region (hg38): 9:129612225-129621101

Links

ENSG00000179058 ∙ NCBI:375759 ∙ ∙ HGNC:23677 ∙ Uniprot:Q5SZB4 ∙ 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 C9orf50 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C9orf50 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				1		1
missense			1	2		3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	3	0

Variants in C9orf50

This is a list of pathogenic ClinVar variants found in the C9orf50 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-129613552-G-A		not specified	Likely benign (Jul 06, 2021)
9-129619764-T-C			Likely benign (Feb 01, 2023)
9-129620195-G-A		not specified	Uncertain significance (Sep 09, 2021)
9-129620377-G-A			Likely benign (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C9orf50	protein_coding	protein_coding	ENST00000372478	7	8552

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.86e-8	0.246	125703	0	28	125731	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.786	164	195	0.842	0.0000116	2664
Missense in Polyphen		26	34.967	0.74355		504
Synonymous	1.02	77	89.2	0.863	0.00000560	958
Loss of Function	0.484	13	15.0	0.865	7.30e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000872	0.0000872
Ashkenazi Jewish	0.00	0.00
East Asian	0.000606	0.000598
Finnish	0.0000497	0.0000462
European (Non-Finnish)	0.0000982	0.0000967
Middle Eastern	0.000606	0.000598
South Asian	0.0000663	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0961
• hipred: N
• hipred_score: 0.180
• ghis: 0.438

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: 1700001O22Rik