C16orf90

Gene

chromosome 16 open reading frame 90

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

MANE transcript

NM_001080524.2

Inheritance

ClinVar variants

U:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr16:3,493,484-3,495,489

External References & Databases

Ensembl (ENSG00000215131)

Transcript & Mutation Effects

hg38 • Region Span ~2.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

multiple congenital anomalies/dysmorphic syndromeLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019042

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to C16orf90 variants in ClinVar

0 Conditions Cataloged

No annotated ClinVar phenotypes.

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080524.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			1 clinvar			1
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	1	0	0	1

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001080524.2	RefSeq	NP_001073993.1	3	MANE Select
ENST00000437192.8	Ensembl	ENSP00000401335.3	3	MANE Select
NM_001353382.1	RefSeq	NP_001340311.1	3	Standard
NM_001353383.1	RefSeq	NP_001340312.1	2	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000437192
Coding exons: 3
Length: 1997
Individuals with no LoFs: 124384
Homozygous LoFs: 0
Heterozygous LoFs: 52
Defined: 124436
p: 0.000209

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0216	105	104	1.01	0.00000595	1147
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00061	0.00058	rare
Latino/Admixed American	0.00024	0.00023	rare
Ashkenazi Jewish	0.0012	0.0012	notable
East Asian	0.000056	0.000056	rare
Finnish	0.00011	0.000093	rare
European (Non-Finnish)	0.00017	0.00016	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.520
RVIS EVS: 0.06
RVIS percentile EVS: 58.53

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N