CGRRF1

protein-coding

cell growth regulator with ring finger domain 1, the group of Ring finger proteins

Gene summary

Predicted to enable zinc ion binding activity. Predicted to be involved in negative regulation of cell growth. Located in endoplasmic reticulum and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_006568.3

Inheritance

—

ClinVar variants

U:35B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr14:54,509,812-54,539,292

External References & Databases

Ensembl (ENSG00000100532)

Transcript & Mutation Effects

hg38 • Region Span ~29.5 kb

Loading mutation effect viewer...

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 CGRRF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 35

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006568.3. 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					1 clinvar	1
missense			35 clinvar		1 clinvar	36
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	35	0	2	37

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006568.3	RefSeq	NP_006559.1	6	MANE Select
ENST00000216420.12	Ensembl	ENSP00000216420.7	6	MANE Select
ENST00000554791.5	Ensembl	ENSP00000451532.1	3	Standard
ENST00000556172.1	Ensembl	ENSP00000470702.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell cycle arrest
negative regulation of cell population proliferation

Molecular Function

metal ion binding

Cellular Component

nucleoplasm
endoplasmic reticulum
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000216420
Coding exons: 6
Length: 29038
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125748
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.223	157	165	0.951	0.00000748	2178
Missense (PolyPhen)		46	50.952	0.9028		694
Synonymous	0.535	58	63.4	0.915	0.00000292	601
Loss of Function	2.14	6	14.9	0.402	6.24e-7	215

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00028	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000033	0.000033	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Able to inhibit growth in several cell lines. {ECO:0000250|UniProtKB:P97587}.;

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.646
RVIS EVS: 0.19
RVIS percentile EVS: 67.03

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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