CHURC1-FNTB

CHURC1-FNTB readthrough

Basic information

Region (hg38): 14:64914484-65061803

Links

ENSG00000125954 ∙ NCBI:100529261 ∙ ∙ HGNC:42960 ∙ ∙ ∙ 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 CHURC1-FNTB gene.

• Inborn genetic diseases (20 variants)
• not provided (9 variants)
• not specified (2 variants)
• Hereditary cancer-predisposing syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHURC1-FNTB 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				2	1	3
missense				2		2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding	1		19	3	3	26
Total	1	0	19	7	5

Highest pathogenic variant AF is 0.0000133

Variants in CHURC1-FNTB

This is a list of pathogenic ClinVar variants found in the CHURC1-FNTB region.

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

Position	Type	Phenotype	Significance	ClinVar
14-64924011-T-A			Likely benign (Jul 06, 2018)
14-64924121-A-G			Benign/Likely benign (Jan 01, 2023)
14-64932149-G-A		not specified	Uncertain significance (May 25, 2022)
14-64932165-G-A		not specified	Uncertain significance (Jun 24, 2022)
14-64932174-G-A		not specified	Uncertain significance (Apr 26, 2023)
14-64932186-A-G		not specified	Uncertain significance (Jan 04, 2022)
14-64932187-G-C		not specified	Uncertain significance (Feb 21, 2024)
14-64932208-G-A		not specified	Uncertain significance (Apr 12, 2023)
14-64939510-C-A		not specified	Uncertain significance (Sep 22, 2022)
14-64939549-C-T		not specified	Uncertain significance (Jan 30, 2024)
14-64939622-G-A		not specified	Uncertain significance (Jun 29, 2023)
14-64939648-T-C		not specified	Uncertain significance (Mar 16, 2022)
14-64939726-T-A		not specified	Uncertain significance (Nov 21, 2023)
14-64939727-C-T		not specified	Uncertain significance (Sep 20, 2023)
14-64942560-C-T		not specified	Uncertain significance (Sep 01, 2021)
14-64942593-C-T		not specified	Uncertain significance (Jan 17, 2023)
14-64942636-C-T		not specified	Uncertain significance (Mar 04, 2024)
14-64942653-G-A		not specified	Uncertain significance (Jan 19, 2024)
14-64942653-G-T		not specified	Uncertain significance (Dec 12, 2023)
14-64942696-G-A		not specified	Uncertain significance (Feb 06, 2023)
14-64942716-A-G		not specified	Uncertain significance (Aug 04, 2023)
14-64948678-T-C		not specified	Uncertain significance (Dec 27, 2023)
14-64950412-G-A		not specified	Likely benign (Sep 16, 2021)
14-64951051-G-A		not specified	Likely benign (Nov 22, 2023)
14-64951082-C-T		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHURC1-FNTB	protein_coding	protein_coding	ENST00000549987	14	147319

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000533	0.999	125720	0	27	125747	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.68	193	271	0.713	0.0000148	3113
Missense in Polyphen		31	83.183	0.37267		944
Synonymous	0.0000387	107	107	1.00	0.00000641	873
Loss of Function	2.82	12	28.2	0.426	0.00000144	328

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000274	0.000273
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000165	0.000163
South Asian	0.00	0.00
Other	0.000194	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential subunit of the farnesyltransferase complex. Catalyzes the transfer of a farnesyl moiety from farnesyl diphosphate to a cysteine at the fourth position from the C- terminus of several proteins having the C-terminal sequence Cys- aliphatic-aliphatic-X. {ECO:0000269|PubMed:12036349, ECO:0000269|PubMed:12825937, ECO:0000269|PubMed:16893176, ECO:0000269|PubMed:19246009, ECO:0000269|PubMed:8494894}.
• Pathway: Signaling by GPCR;Signal Transduction;G alpha (i) signalling events;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling (Consensus)

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.223
• ghis: 0.403

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene ontology

• Biological process: multicellular organism development;protein prenylation;protein farnesylation;positive regulation of transcription, DNA-templated
• Cellular component: protein farnesyltransferase complex
• Molecular function: protein farnesyltransferase activity;zinc ion binding