CCER2

coiled-coil glutamate rich protein 2

Basic information

Region (hg38): 19:38908980-38912186

Links

ENSG00000262484 ∙ NCBI:643669 ∙ OMIM:617634 ∙ HGNC:44662 ∙ Uniprot:I3L3R5 ∙ 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 CCER2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCER2 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	1	3
missense			4	2	6	12
nonsense						0
start loss						0
frameshift						0
inframe indel			1	1	1	3
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				2	1	3
Total	0	0	5	7	9

Variants in CCER2

This is a list of pathogenic ClinVar variants found in the CCER2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-38909266-C-T			Likely benign (Sep 06, 2024)
19-38909267-G-A			Uncertain significance (Dec 02, 2024)
19-38909277-CCTT-C			Uncertain significance (Feb 03, 2025)
19-38910572-C-T			Likely benign (Oct 13, 2022)
19-38910579-T-G			Benign (Oct 06, 2024)
19-38910611-CTGG-C			Benign (Oct 06, 2024)
19-38910611-CTGGTGGTGG-C			Likely benign (Apr 09, 2023)
19-38910648-C-T			Likely benign (Feb 23, 2024)
19-38910652-T-C			Likely benign (Nov 25, 2024)
19-38910670-C-T			Uncertain significance (Dec 27, 2022)
19-38910690-C-T			Uncertain significance (Oct 26, 2024)
19-38910796-C-T			Benign (Oct 06, 2024)
19-38910804-C-T			Likely benign (Mar 16, 2024)
19-38910827-C-G			Likely benign (Mar 26, 2024)
19-38910846-C-T			Uncertain significance (Feb 23, 2024)
19-38911045-C-T			Benign (Nov 20, 2024)
19-38911061-G-A			Likely benign (Jun 15, 2023)
19-38911072-T-A			Benign (Dec 13, 2024)
19-38911082-C-G			Benign (Oct 06, 2024)
19-38911553-G-C			Likely benign (Aug 20, 2024)
19-38911555-G-T			Likely benign (Oct 13, 2023)
19-38911656-G-T			Benign (Jan 27, 2025)
19-38911815-C-G			Benign (Feb 03, 2025)
19-38912079-C-T			Benign (Nov 13, 2023)
19-38912080-G-A			Likely benign (Dec 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCER2	protein_coding	protein_coding	ENST00000571838	5	3179

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00397	0.868	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.260	114	122	0.934	0.00000736	1685
Missense in Polyphen		25	24.318	1.028		297
Synonymous	1.10	42	52.1	0.807	0.00000324	504
Loss of Function	1.28	5	9.19	0.544	4.24e-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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.180
• ghis: 0.490

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccer2

Gene ontology

• Cellular component: extracellular region