C9orf43

chromosome 9 open reading frame 43

Basic information

Region (hg38): 9:113410053-113429690

Links

ENSG00000157653 ∙ NCBI:257169 ∙ ∙ HGNC:23570 ∙ Uniprot:Q8TAL5 ∙ 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 C9orf43 gene.

• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C9orf43 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			2	1		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	2	1	0

Variants in C9orf43

This is a list of pathogenic ClinVar variants found in the C9orf43 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-113410107-G-A		not specified	Uncertain significance (Jun 30, 2022)
9-113410128-C-T		not specified	Uncertain significance (Aug 16, 2022)
9-113410136-G-A		not specified	Uncertain significance (Sep 22, 2021)
9-113419113-C-T		not specified	Uncertain significance (Sep 27, 2021)
9-113422578-C-T		not specified	Likely benign (Oct 06, 2021)
9-113423398-G-A		not specified	Uncertain significance (Nov 08, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C9orf43	protein_coding	protein_coding	ENST00000288462	13	19631

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.36e-11	0.552	108149	808	16790	125747	0.0726

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.172	243	251	0.969	0.0000130	3035
Missense in Polyphen		50	58.759	0.85093		741
Synonymous	-0.763	104	94.6	1.10	0.00000544	845
Loss of Function	1.33	20	27.5	0.726	0.00000150	307

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0516	0.0515
Ashkenazi Jewish	0.0569	0.0566
East Asian	0.0483	0.0480
Finnish	0.118	0.119
European (Non-Finnish)	0.0891	0.0888
Middle Eastern	0.0483	0.0480
South Asian	0.0756	0.0743
Other	0.0700	0.0699

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.915
• rvis_EVS: 1.44
• rvis_percentile_EVS: 95.08

Haploinsufficiency Scores

• pHI: 0.0257
• hipred: N
• hipred_score: 0.123

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: 4933430I17Rik
• Phenotype: skeleton phenotype; limbs/digits/tail phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Molecular function: protein binding