C9orf131

chromosome 9 open reading frame 131

Basic information

Region (hg38): 9:35041094-35045986

Links

ENSG00000174038 ∙ NCBI:138724 ∙ ∙ HGNC:31418 ∙ Uniprot:Q5VYM1 ∙ 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 C9orf131 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C9orf131 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in C9orf131

This is a list of pathogenic ClinVar variants found in the C9orf131 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-35042286-C-A		not specified	Uncertain significance (Oct 29, 2021)
9-35042379-T-A		not specified	Uncertain significance (Aug 04, 2021)
9-35042400-T-C		not specified	Uncertain significance (Jul 06, 2021)
9-35043606-C-G		not specified	Uncertain significance (Sep 17, 2021)
9-35043671-G-C		not specified	Uncertain significance (Nov 09, 2021)
9-35043690-G-C		not specified	Uncertain significance (Oct 12, 2021)
9-35044509-T-C		not specified	Uncertain significance (Jul 09, 2021)
9-35045056-T-G		not specified	Uncertain significance (Nov 10, 2021)
9-35045184-G-A		not specified	Uncertain significance (Oct 29, 2021)
9-35045465-G-C			Uncertain significance (Oct 16, 2019)
9-35045566-C-A		not specified	Likely benign (Jul 15, 2021)
9-35045573-G-A		not specified	Uncertain significance (Jun 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C9orf131	protein_coding	protein_coding	ENST00000312292	2	4897

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.63e-18	0.00586	125549	2	197	125748	0.000792

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.68	654	544	1.20	0.0000272	6954
Missense in Polyphen		151	122.83	1.2294		1798
Synonymous	-0.771	232	218	1.07	0.0000114	2308
Loss of Function	0.110	27	27.6	0.977	0.00000132	329

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00138	0.00137
Ashkenazi Jewish	0.00	0.00
East Asian	0.000490	0.000489
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000590	0.000589
Middle Eastern	0.000490	0.000489
South Asian	0.00281	0.00275
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.982
• rvis_EVS: 0.61
• rvis_percentile_EVS: 82.94

Haploinsufficiency Scores

• pHI: 0.0454
• hipred: N
• hipred_score: 0.123
• ghis: 0.425

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: 1700022I11Rik