CCER1

coiled-coil glutamate rich protein 1

Basic information

Region (hg38): 12:90905622-90955176

Previous symbols: [ "C12orf12" ]

Links

ENSG00000197651 ∙ NCBI:196477 ∙ ∙ HGNC:28373 ∙ Uniprot:Q8TC90 ∙ 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 CCER1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCER1 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			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	0

Variants in CCER1

This is a list of pathogenic ClinVar variants found in the CCER1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-90953530-T-C		not specified	Uncertain significance (Jan 30, 2025)
12-90953578-T-A		not specified	Uncertain significance (Aug 17, 2022)
12-90953615-C-G		not specified	Uncertain significance (Dec 07, 2024)
12-90953646-G-A		not specified	Uncertain significance (Nov 21, 2022)
12-90953692-C-G		not specified	Uncertain significance (Oct 12, 2021)
12-90953841-C-T		not specified	Uncertain significance (Oct 13, 2023)
12-90953850-T-G		not specified	Uncertain significance (Feb 03, 2025)
12-90953939-G-T		not specified	Uncertain significance (Apr 07, 2023)
12-90953978-C-G		not specified	Uncertain significance (Dec 07, 2021)
12-90953992-A-G		not specified	Uncertain significance (Feb 09, 2023)
12-90954070-C-T		not specified	Uncertain significance (Jul 14, 2022)
12-90954093-T-G		not specified	Uncertain significance (Jan 04, 2022)
12-90954133-G-C		not specified	Uncertain significance (Apr 22, 2022)
12-90954134-C-G		not specified	Uncertain significance (Jan 31, 2023)
12-90954153-A-T		not specified	Uncertain significance (Feb 25, 2025)
12-90954155-C-G		not specified	Uncertain significance (Aug 28, 2024)
12-90954234-G-C		not specified	Uncertain significance (Nov 20, 2024)
12-90954267-G-T		not specified	Uncertain significance (Dec 14, 2024)
12-90954279-C-A		not specified	Uncertain significance (Jul 20, 2022)
12-90954298-C-A		not specified	Uncertain significance (Apr 18, 2023)
12-90954319-G-C		not specified	Uncertain significance (May 13, 2022)
12-90954457-G-C		not specified	Uncertain significance (Apr 27, 2022)
12-90954471-G-A		not specified	Uncertain significance (Mar 25, 2024)
12-90954487-C-G		not specified	Uncertain significance (May 11, 2022)
12-90954502-C-A		not specified	Likely benign (Jun 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCER1	protein_coding	protein_coding	ENST00000358859	1	49555

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000420	0.857	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.637	225	254	0.887	0.0000161	2637
Missense in Polyphen		52	64.869	0.80162		469
Synonymous	0.668	102	111	0.919	0.00000795	765
Loss of Function	1.38	9	14.7	0.612	8.73e-7	135

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

Recessive Scores

• pRec: 0.0854

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.290
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccer1

Gene ontology

• Molecular function: protein binding