CHURC1-FNTB

protein-coding

CHURC1-FNTB readthrough

Gene summary

This locus represents naturally occurring read-through transcription between the neighboring CHURC1 (churchill domain containing 1) and FNTB (farnesyltransferase, CAAX box, beta) on chromosome 14. The read-through transcript produces a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Feb 2011]

MANE transcript

N/A

Inheritance

—

ClinVar variants

B:6

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr14:64,914,485-65,061,803

External References & Databases

Ensembl (ENSG00000125954)

NCBI Gene (100529261)

HGNC:42960

GenCC

ClinVar (CHURC1-FNTB)

Transcript & Mutation Effects

hg38 • Region Span ~147.3 kb

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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 CHURC1-FNTB variants in ClinVar

4 Conditions Cataloged

Inborn genetic diseasesTotal: 20

not providedTotal: 9

not specifiedTotal: 2

Hereditary cancer-predisposing syndromeTotal: 1

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				2 clinvar	1 clinvar	3
missense				2 clinvar		2
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)					1 clinvar	1
Total	0	0	0	4	2	6

Highest pathogenic variant AF is 0.0000133216

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001202558.2	RefSeq	NP_001189487.1	12	Standard
NM_001202559.1	RefSeq	NP_001189488.1	14	Standard
ENST00000549987.1	Ensembl	ENSP00000447121.2	14	Standard
ENST00000551823.1	Ensembl	ENSP00000449709.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signaling by GPCR
Signal Transduction
G alpha (i) signalling events
Inactivation, recovery and regulation of the phototransduction cascade
The phototransduction cascade

Biological Process

multicellular organism development
protein prenylation
protein farnesylation
positive regulation of transcription, DNA-templated

Molecular Function

protein farnesyltransferase activity
zinc ion binding

Cellular Component

protein farnesyltransferase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000549987
Coding exons: 14
Length: 147319
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125747
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.68	193	271	0.713	0.0000148	3113
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.00021	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0	0.0	absent
Other	0.00019	0.00016	rare

dbNSFP Gene Annotations

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}.;

Intolerance Scores

RVIS EVS: -0.16
RVIS percentile EVS: 41.91

Essentials

Indispensability pred.: N
Indispensability score: 0.114