C16orf90

chromosome 16 open reading frame 90

Basic information

Region (hg38): 16:3493484-3495489

Links

ENSG00000215131 ∙ NCBI:646174 ∙ ∙ HGNC:34455 ∙ Uniprot:A8MZG2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• multiple congenital anomalies/dysmorphic syndrome (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C16orf90 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C16orf90 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C16orf90	protein_coding	protein_coding	ENST00000437192	3	1997

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00135	0.672	124384	0	52	124436	0.000209

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0216	105	104	1.01	0.00000595	1147
Missense in Polyphen		26	26.665	0.97505		306
Synonymous	-0.623	48	42.8	1.12	0.00000227	387
Loss of Function	0.695	5	6.98	0.716	3.85e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000853	0.000821
Ashkenazi Jewish	0.00124	0.00120
East Asian	0.0000564	0.0000556
Finnish	0.000107	0.0000928
European (Non-Finnish)	0.000167	0.000160
Middle Eastern	0.0000564	0.0000556
South Asian	0.0000328	0.0000327
Other	0.000169	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.520
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: 1700037C18Rik