CFAP298-TCP10L

protein-coding

CFAP298-TCP10L readthrough

Gene summary

This locus represents naturally occurring readthrough transcription between the neighboring chromosome 21 open reading frame 59 (C21orf59) and TCP10L (t-complex 10 like) genes on chromosome 21. Readthrough transcripts may encode a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Apr 2017]

Previous symbols:

LINC00846
C21orf77

MANE transcript

N/A

Inheritance

—

ClinVar variants

P:4U:43B:34

Top phenotype

Primary ciliary dyskinesia 26

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr21:32,402,511-32,612,865

External References & Databases

Ensembl (ENSG00000265590)

NCBI Gene (110091775)

HGNC:54636

GenCC

ClinVar (CFAP298-TCP10L)

Transcript & Mutation Effects

hg38 • Region Span ~210.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CFAP298-TCP10L variants in ClinVar

2 Conditions Cataloged

not providedTotal: 5

Primary ciliary dyskinesia 26Total: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . 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			1 clinvar	27 clinvar	2 clinvar	30
missense			42 clinvar	4 clinvar		46
nonsense		1 clinvar				1
start loss						0
frameshift	2 clinvar				1 clinvar	3
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	2	2	43	31	3	81

Highest pathogenic variant AF is 0.000210054

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001350338.2	RefSeq	NP_001337267.1	8	Standard
ENST00000431216.5	Ensembl	ENSP00000391771.1	8	Standard
ENST00000553001.2	Ensembl	ENSP00000446874.2	6	Standard
ENST00000673072.2	Ensembl	ENSP00000500800.2	8	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000553001
Coding exons: 7
Length: 33460
Individuals with no LoFs: 125636
Homozygous LoFs: 0
Heterozygous LoFs: 111
Defined: 125747
p: 0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.493	152	170	0.894	0.00000939	1934
Missense (PolyPhen)		40	52.923	0.75581		601
Synonymous	-0.602	78	71.5	1.09	0.00000467	555
Loss of Function	1.40	12	18.5	0.648	0.00000104	197

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00080	0.00080	rare
Latino/Admixed American	0.00032	0.00032	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.00055	0.00055	rare
European (Non-Finnish)	0.00052	0.00051	rare
South Asian	0.00039	0.00039	rare
Other	0.00016	0.00016	rare