C20orf96

chromosome 20 open reading frame 96

Basic information

Region (hg38): 20:270863-290778

Links

ENSG00000196476 ∙ NCBI:140680 ∙ ∙ HGNC:16227 ∙ Uniprot:Q9NUD7 ∙ 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 C20orf96 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C20orf96 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			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	1

Variants in C20orf96

This is a list of pathogenic ClinVar variants found in the C20orf96 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-278354-C-T		not specified	Uncertain significance (Jul 06, 2021)
20-279210-G-T		not specified	Likely benign (Nov 09, 2021)
20-279213-G-C		not specified	Uncertain significance (Aug 17, 2021)
20-279299-C-A		not specified	Uncertain significance (Aug 13, 2021)
20-289563-T-C			Benign (Apr 10, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C20orf96	protein_coding	protein_coding	ENST00000360321	11	19887

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.18e-14	0.0223	125253	1	494	125748	0.00197

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.506	224	204	1.10	0.0000112	2408
Missense in Polyphen		51	47.144	1.0818		648
Synonymous	0.129	72	73.4	0.981	0.00000393	630
Loss of Function	0.188	22	23.0	0.958	0.00000115	259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00980	0.00976
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00471	0.00472
European (Non-Finnish)	0.00118	0.00118
Middle Eastern	0.000109	0.000109
South Asian	0.00124	0.00124
Other	0.00212	0.00212

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.922
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.0274
• hipred: N
• hipred_score: 0.123
• ghis: 0.495

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: 6820408C15Rik