CFAP298-TCP10L

CFAP298-TCP10L readthrough

Basic information

Region (hg38): 21:32402511-32612865

Previous symbols: [ "LINC00846", "C21orf77" ]

Links

ENSG00000265590 ∙ NCBI:110091775 ∙ ∙ HGNC:54636 ∙ ∙ ∙ 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 CFAP298-TCP10L gene.

• not provided (5 variants)
• Primary ciliary dyskinesia 26 (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP298-TCP10L 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			1	26	2	29
missense			36	4		40
nonsense		1				1
start loss						0
frameshift	2				1	3
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1				1
splice region			3	3		6
non coding	4		42	30	17	93
Total	6	2	80	60	20

Highest pathogenic variant AF is 0.000210

Variants in CFAP298-TCP10L

This is a list of pathogenic ClinVar variants found in the CFAP298-TCP10L region.

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

Position	Type	Phenotype	Significance	ClinVar
21-32412896-C-T		not specified	Uncertain significance (Jan 16, 2024)
21-32412899-G-A		not specified	Uncertain significance (Dec 21, 2022)
21-32412917-C-T		not specified	Uncertain significance (Oct 27, 2023)
21-32412920-C-A			Likely benign (Jun 22, 2023)
21-32412927-T-C		not specified	Uncertain significance (Sep 14, 2023)
21-32412977-T-G		not specified	Uncertain significance (Feb 02, 2022)
21-32412984-A-T		not specified	Uncertain significance (Jan 08, 2024)
21-32453359-G-C		not specified	Uncertain significance (Apr 18, 2023)
21-32453378-A-G		not specified	Uncertain significance (Aug 09, 2021)
21-32453386-C-T		not specified	Uncertain significance (Jan 26, 2023)
21-32453407-C-G		not specified	Uncertain significance (Jul 14, 2021)
21-32457648-A-T		not specified	Uncertain significance (Feb 27, 2024)
21-32457651-C-T		not specified	Uncertain significance (Apr 27, 2022)
21-32457652-G-A		not specified	Uncertain significance (Nov 08, 2022)
21-32467740-C-G		not specified	Uncertain significance (Mar 16, 2022)
21-32467744-A-G		not specified	Uncertain significance (Apr 26, 2024)
21-32467842-C-A		not specified	Uncertain significance (Oct 26, 2021)
21-32467842-C-G		not specified	Uncertain significance (Jul 20, 2021)
21-32467843-C-G		not specified	Uncertain significance (Mar 16, 2022)
21-32495163-C-T			Benign (Jul 16, 2018)
21-32495164-G-T		not specified	Uncertain significance (Aug 13, 2021)
21-32501436-C-T		not specified	Uncertain significance (Sep 14, 2022)
21-32503926-G-A		not specified	Uncertain significance (May 24, 2024)
21-32503934-T-G		not specified	Uncertain significance (Jul 08, 2022)
21-32504009-A-G		not specified	Uncertain significance (Jul 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP298-TCP10L	protein_coding	protein_coding	ENST00000553001	7	33460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000119	0.821	125636	0	111	125747	0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.493	152	170	0.894	0.00000939	1934
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00112	0.00112
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.000554	0.000554
European (Non-Finnish)	0.000520	0.000510
Middle Eastern	0.000217	0.000217
South Asian	0.000392	0.000392
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP