C16orf96

chromosome 16 open reading frame 96

Basic information

Region (hg38): 16:4556340-4600758

Links

ENSG00000205832 ∙ NCBI:342346 ∙ ∙ HGNC:40031 ∙ Uniprot:A6NNT2 ∙ 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 C16orf96 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C16orf96 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			13	6	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	9	1

Variants in C16orf96

This is a list of pathogenic ClinVar variants found in the C16orf96 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-4556529-G-A		not specified	Uncertain significance (Oct 06, 2021)
16-4556582-C-T			Likely benign (Dec 01, 2022)
16-4556604-A-G			Likely benign (Apr 01, 2023)
16-4556732-C-T			Likely benign (Aug 01, 2022)
16-4556871-C-T		not specified	Uncertain significance (Aug 16, 2021)
16-4575003-C-G		not specified	Uncertain significance (Aug 06, 2021)
16-4575011-G-A		not specified	Uncertain significance (Jul 14, 2021)
16-4575270-G-A		not specified	Uncertain significance (Oct 14, 2021)
16-4575291-G-A		not specified	Likely benign (Aug 10, 2021)
16-4575350-G-A			Likely benign (Feb 01, 2024)
16-4575541-C-T		not specified	Likely benign (Aug 10, 2021)
16-4575663-C-T		not specified	Uncertain significance (Sep 17, 2021)
16-4575930-C-T			Benign (Jun 06, 2017)
16-4576197-G-A		not specified	Uncertain significance (Sep 16, 2021)
16-4576452-G-A		not specified	Likely benign (Jul 14, 2021)
16-4587055-T-A		not specified	Uncertain significance (Oct 26, 2021)
16-4588221-G-A		not specified	Uncertain significance (Sep 27, 2021)
16-4588317-G-A			Likely benign (Apr 01, 2023)
16-4592318-C-T		not specified	Uncertain significance (Aug 16, 2021)
16-4592342-C-T		not specified	Uncertain significance (Aug 28, 2021)
16-4593291-G-A		not specified	Uncertain significance (Jul 14, 2021)
16-4594481-G-A			Likely benign (Feb 01, 2024)
16-4600136-C-T		not specified	Uncertain significance (Aug 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C16orf96	protein_coding	protein_coding	ENST00000444310	16	44225

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.58e-21	0.0403	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.768	599	654	0.915	0.0000377	7382
Missense in Polyphen		104	121.65	0.85489		1426
Synonymous	3.17	209	276	0.757	0.0000172	2351
Loss of Function	1.14	36	44.2	0.815	0.00000226	518

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 3.56
• rvis_percentile_EVS: 99.5

Haploinsufficiency Scores

• 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	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: 4930562C15Rik