C2orf78

chromosome 2 open reading frame 78

Basic information

Region (hg38): 2:73784183-73817148

Links

ENSG00000187833 ∙ NCBI:388960 ∙ ∙ HGNC:34349 ∙ Uniprot:A6NCI8 ∙ 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 C2orf78 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C2orf78 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in C2orf78

This is a list of pathogenic ClinVar variants found in the C2orf78 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-73784352-G-C		not specified	Uncertain significance (Aug 02, 2021)
2-73814097-T-C		not specified	Uncertain significance (Sep 16, 2021)
2-73815271-C-T		not specified	Uncertain significance (Sep 16, 2021)
2-73815809-G-A		not specified	Uncertain significance (Jun 21, 2021)
2-73815847-G-A		not specified	Uncertain significance (Jul 20, 2021)
2-73816942-G-C		not specified	Uncertain significance (Oct 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C2orf78	protein_coding	protein_coding	ENST00000409561	3	32959

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.76e-7	0.985	124623	0	26	124649	0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.402	447	472	0.948	0.0000236	5976
Missense in Polyphen		105	121.98	0.86077		1698
Synonymous	0.875	165	180	0.917	0.00000885	1931
Loss of Function	2.23	14	26.3	0.532	0.00000144	335

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000332	0.000332
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000134	0.000133
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.287
• rvis_EVS: -0.09
• rvis_percentile_EVS: 47.12

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.173

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