CGGBP1

CGG triplet repeat binding protein 1

Basic information

Region (hg38): 3:88051943-88149885

Links

ENSG00000163320 ∙ NCBI:8545 ∙ OMIM:603363 ∙ HGNC:1888 ∙ Uniprot:Q9UFW8 ∙ 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 CGGBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CGGBP1 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
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			23	1		24
Total	0	0	24	1	0

Variants in CGGBP1

This is a list of pathogenic ClinVar variants found in the CGGBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-88055858-T-C		not specified	Uncertain significance (Feb 06, 2024)
3-88139375-A-C		not specified	Uncertain significance (Jul 12, 2023)
3-88139396-T-C		not specified	Uncertain significance (Jul 05, 2023)
3-88139477-T-C		not specified	Uncertain significance (Feb 15, 2023)
3-88139584-G-C		not specified	Uncertain significance (Jan 22, 2024)
3-88139600-C-T		not specified	Uncertain significance (Apr 12, 2022)
3-88139605-T-C		not specified	Uncertain significance (Dec 22, 2023)
3-88139639-A-G		not specified	Uncertain significance (Apr 17, 2024)
3-88139699-T-C		not specified	Uncertain significance (Feb 17, 2024)
3-88139836-G-A		not specified	Likely benign (Jul 12, 2023)
3-88139848-A-G		not specified	Uncertain significance (Aug 08, 2023)
3-88139986-A-G		not specified	Uncertain significance (Jun 11, 2024)
3-88140019-T-G		not specified	Uncertain significance (Mar 01, 2023)
3-88140089-A-G		not specified	Uncertain significance (Dec 20, 2023)
3-88140403-G-T		not specified	Uncertain significance (Dec 22, 2023)
3-88140430-T-A		not specified	Uncertain significance (Nov 29, 2021)
3-88140449-G-A		not specified	Uncertain significance (Dec 17, 2023)
3-88140458-G-A		not specified	Uncertain significance (Jan 23, 2024)
3-88140469-A-G		not specified	Uncertain significance (Sep 27, 2021)
3-88140515-C-T		not specified	Uncertain significance (Dec 18, 2023)
3-88140553-G-A		not specified	Uncertain significance (Jan 08, 2024)
3-88140557-T-C		not specified	Uncertain significance (May 02, 2024)
3-88140596-T-C		not specified	Uncertain significance (Jun 09, 2022)
3-88140647-C-T		not specified	Uncertain significance (Mar 08, 2024)
3-88140744-G-C		not specified	Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CGGBP1	protein_coding	protein_coding	ENST00000398392	1	97942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.818	0.178	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	52	95.0	0.547	0.00000517	1086
Missense in Polyphen		1	14.401	0.06944		193
Synonymous	-0.955	39	32.1	1.21	0.00000146	336
Loss of Function	2.20	0	5.63	0.00	4.53e-7	55

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to nonmethylated 5'-d(CGG)(n)-3' trinucleotide repeats in the FMR1 promoter. May play a role in regulating FMR1 promoter. {ECO:0000269|PubMed:9201980}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.194
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.224
• hipred: Y
• hipred_score: 0.543
• ghis: 0.698

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Mouse Genome Informatics

• Gene name: Cggbp1

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription repressor activity, RNA polymerase II-specific;double-stranded DNA binding;protein binding;identical protein binding