TVP23C-CDRT4

TVP23C-CDRT4 readthrough

Basic information

Region (hg38): 17:15436020-15563561

Previous symbols: [ "FAM18B2-CDRT4" ]

Links

ENSG00000259024 ∙ NCBI:100533496 ∙ ∙ HGNC:42961 ∙ ∙ ∙ 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 TVP23C-CDRT4 gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TVP23C-CDRT4 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			1	1		2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding			1			1
Total	0	0	3	1	0

Variants in TVP23C-CDRT4

This is a list of pathogenic ClinVar variants found in the TVP23C-CDRT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-15437787-T-C		not specified	Uncertain significance (Aug 14, 2023)
17-15437804-A-G		not specified	Uncertain significance (Jul 06, 2021)
17-15437813-C-A		not specified	Uncertain significance (Feb 16, 2023)
17-15437813-C-T		not specified	Uncertain significance (Mar 03, 2022)
17-15437922-C-T		not specified	Likely benign (Jan 24, 2024)
17-15437942-G-T		not specified	Uncertain significance (Feb 15, 2023)
17-15438053-T-C		not specified	Uncertain significance (Mar 19, 2024)
17-15438143-G-A		not specified	Uncertain significance (Jan 04, 2022)
17-15438174-G-A		not specified	Uncertain significance (May 17, 2023)
17-15440223-T-C		not specified	Uncertain significance (Jan 16, 2024)
17-15440225-C-T		not specified	Likely benign (Jun 24, 2022)
17-15503146-T-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TVP23C-CDRT4	protein_coding	protein_coding	ENST00000522212	6	127538

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.74e-7	0.319	125686	0	62	125748	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0635	83	84.6	0.981	0.00000428	1082
Missense in Polyphen		19	15.782	1.2039		242
Synonymous	0.0229	30	30.2	0.995	0.00000162	288
Loss of Function	0.383	10	11.4	0.877	5.50e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000301	0.000301
Ashkenazi Jewish	0.00	0.00
East Asian	0.000845	0.000816
Finnish	0.000786	0.000786
European (Non-Finnish)	0.000172	0.000167
Middle Eastern	0.000845	0.000816
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.139
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium