C16orf78

chromosome 16 open reading frame 78

Basic information

Region (hg38): 16:49373803-49399431

Links

ENSG00000166152 ∙ NCBI:123970 ∙ ∙ HGNC:28479 ∙ Uniprot:Q8WTQ4 ∙ 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 C16orf78 gene.

• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C16orf78 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			2
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	0	0

Variants in C16orf78

This is a list of pathogenic ClinVar variants found in the C16orf78 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-49377843-C-T		not specified	Uncertain significance (Aug 30, 2021)
16-49396449-C-T		not specified	Uncertain significance (Sep 17, 2021)
16-49396480-G-A		not specified	Uncertain significance (Sep 15, 2021)
16-49399246-G-A		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C16orf78	protein_coding	protein_coding	ENST00000299191	5	25609

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000594	0.703	125620	2	124	125746	0.000501

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00565	155	155	0.999	0.00000858	1751
Missense in Polyphen		47	37.713	1.2462		474
Synonymous	0.270	53	55.6	0.954	0.00000315	464
Loss of Function	1.08	10	14.4	0.694	9.46e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00572	0.00528
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000326	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.000326	0.000326
South Asian	0.000264	0.000261
Other	0.000507	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.820
• rvis_EVS: 1.11
• rvis_percentile_EVS: 92.04

Haploinsufficiency Scores

• pHI: 0.0366
• 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: 4933402J07Rik

Gene ontology

• Cellular component: nucleus