CCER1

protein-coding

coiled-coil glutamate rich protein 1

Gene summary

Predicted to be involved in sperm DNA condensation. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C12orf12

MANE transcript

NM_152638.4

Inheritance

—

ClinVar variants

U:63B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr12:90,905,622-90,955,176

External References & Databases

Ensembl (ENSG00000197651)

Transcript & Mutation Effects

hg38 • Region Span ~49.6 kb

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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 CCER1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 65

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152638.4. 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						0
missense			63 clinvar	2 clinvar		65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	63	2	0	65

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152638.4	RefSeq	NP_689851.1	1	MANE Select
ENST00000358859.3	Ensembl	ENSP00000351727.2	1	MANE Select
ENST00000549707.1	Ensembl	ENSP00000446773.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358859
Coding exons: 1
Length: 49555
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.637	225	254	0.887	0.0000161	2637
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0854

Intolerance Scores

RVIS EVS: 0.08
RVIS percentile EVS: 60.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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