CHFR

checkpoint with forkhead and ring finger domains, the group of Ring finger proteins

Basic information

Region (hg38): 12:132822187-132956304

Links

ENSG00000072609 ∙ NCBI:55743 ∙ OMIM:605209 ∙ HGNC:20455 ∙ Uniprot:Q96EP1 ∙ AlphaFold ∙ 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 CHFR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHFR 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	2
missense			54	1		55
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	54	1	2

Variants in CHFR

This is a list of pathogenic ClinVar variants found in the CHFR region.

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

Position	Type	Phenotype	Significance	ClinVar
12-132841588-T-C		not specified	Uncertain significance (Oct 05, 2021)
12-132844057-G-A		not specified	Uncertain significance (Aug 13, 2021)
12-132844059-T-C		not specified	Uncertain significance (Sep 22, 2023)
12-132844111-C-T		not specified	Uncertain significance (Jul 14, 2023)
12-132844122-G-A		not specified	Uncertain significance (Jun 18, 2021)
12-132847072-G-A		not specified	Uncertain significance (Dec 07, 2023)
12-132847076-C-A		not specified	Uncertain significance (Jan 10, 2023)
12-132847085-C-T		not specified	Uncertain significance (Mar 13, 2023)
12-132847123-A-G		not specified	Uncertain significance (May 30, 2024)
12-132848649-G-A		not specified	Uncertain significance (May 01, 2022)
12-132848673-G-T		not specified	Uncertain significance (Nov 28, 2023)
12-132848720-C-T			Benign (May 09, 2018)
12-132848721-G-A		not specified	Uncertain significance (Jun 11, 2021)
12-132851638-G-A		not specified	Uncertain significance (May 15, 2024)
12-132851648-C-T		not specified	Uncertain significance (Jul 31, 2024)
12-132851663-G-A		not specified	Uncertain significance (Feb 22, 2023)
12-132851694-C-T			Benign (May 09, 2018)
12-132853446-C-T		not specified	Uncertain significance (Nov 09, 2021)
12-132853460-G-A		not specified	Likely benign (Jun 24, 2022)
12-132853572-G-A			Likely pathogenic (Oct 12, 2022)
12-132856519-G-A		not specified	Uncertain significance (Dec 03, 2024)
12-132856579-A-C		not specified	Uncertain significance (Dec 20, 2023)
12-132857435-G-C		not specified	Uncertain significance (May 16, 2023)
12-132857471-C-T		not specified	Uncertain significance (Dec 27, 2023)
12-132857480-G-A		not specified	Uncertain significance (Apr 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHFR	protein_coding	protein_coding	ENST00000432561	17	134118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000787	0.999	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	325	392	0.828	0.0000250	4267
Missense in Polyphen		86	126.53	0.67969		1323
Synonymous	0.221	166	170	0.978	0.0000121	1288
Loss of Function	3.64	12	35.4	0.339	0.00000159	436

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.0000548	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000229	0.000229
Middle Eastern	0.0000548	0.0000544
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that functions in the antephase checkpoint by actively delaying passage into mitosis in response to microtubule poisons. Acts in early prophase before chromosome condensation, when the centrosome move apart from each other along the periphery of the nucleus. Probably involved in signaling the presence of mitotic stress caused by microtubule poisons by mediating the 'Lys-48'-linked ubiquitination of target proteins, leading to their degradation by the proteasome. Promotes the ubiquitination and subsequent degradation of AURKA and PLK1. Probably acts as a tumor suppressor, possibly by mediating the polyubiquitination of HDAC1, leading to its degradation. May also promote the formation of 'Lys-63'-linked polyubiquitin chains and functions with the specific ubiquitin-conjugating UBC13-MMS2 (UBE2N-UBE2V2) heterodimer. Substrates that are polyubiquitinated at 'Lys-63' are usually not targeted for degradation, but are rather involved in signaling cellular stress. {ECO:0000269|PubMed:10935642, ECO:0000269|PubMed:11807090, ECO:0000269|PubMed:11912157, ECO:0000269|PubMed:14562038, ECO:0000269|PubMed:14694445, ECO:0000269|PubMed:18172500, ECO:0000269|PubMed:19182791}.

Recessive Scores

• pRec: 0.161

Intolerance Scores

• loftool: 0.645
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.93

Haploinsufficiency Scores

• pHI: 0.0914
• hipred: Y
• hipred_score: 0.744
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.855

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chfr
• Phenotype: neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: protein polyubiquitination;ubiquitin-dependent protein catabolic process;mitotic cell cycle checkpoint;protein ubiquitination;modification-dependent protein catabolic process;positive regulation of protein ubiquitination;protein destabilization;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;cell division
• Cellular component: nucleus;PML body
• Molecular function: nucleotide binding;ubiquitin-protein transferase activity;protein binding;metal ion binding;ubiquitin protein ligase activity