C3orf20

chromosome 3 open reading frame 20

Basic information

Region (hg38): 3:14675141-14773036

Links

ENSG00000131379 ∙ NCBI:84077 ∙ OMIM:619992 ∙ HGNC:25320 ∙ Uniprot:Q8ND61 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neuromyelitis optica (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C3orf20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C3orf20 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				3		3
missense			4	3		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	6	0

Variants in C3orf20

This is a list of pathogenic ClinVar variants found in the C3orf20 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-14683157-C-T			Likely benign (Sep 01, 2022)
3-14683191-A-G		not specified	Likely benign (Sep 27, 2021)
3-14684270-G-A			Likely benign (Jun 01, 2022)
3-14703199-G-A		not specified	Uncertain significance (Aug 13, 2021)
3-14714023-G-A		not specified	Likely benign (Jun 22, 2021)
3-14714155-A-G			not provided (-)
3-14715295-A-G			Likely benign (Sep 01, 2022)
3-14721744-C-T		not specified	Uncertain significance (Jul 26, 2021)
3-14728646-G-A		not specified	Likely benign (Nov 16, 2021)
3-14757381-C-T		not specified	Uncertain significance (Sep 16, 2021)
3-14757403-G-A			not provided (-)
3-14759978-G-A		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C3orf20	protein_coding	protein_coding	ENST00000253697	15	97936

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.38e-21	0.0128	125433	1	314	125748	0.00125

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.429	487	514	0.947	0.0000291	5864
Missense in Polyphen		133	167.76	0.79281		2105
Synonymous	0.656	192	204	0.942	0.0000112	1815
Loss of Function	0.809	35	40.6	0.863	0.00000216	480

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00739	0.00740
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000435	0.000435
Finnish	0.000231	0.000231
European (Non-Finnish)	0.00114	0.00113
Middle Eastern	0.000435	0.000435
South Asian	0.000329	0.000327
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.990
• rvis_EVS: 1.12
• rvis_percentile_EVS: 92.1

Haploinsufficiency Scores

• pHI: 0.235
• 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	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: 4930590J08Rik

Gene ontology

• Cellular component: cytoplasm;integral component of membrane