CCDC87

coiled-coil domain containing 87

Basic information

Region (hg38): 11:66590176-66593063

Links

ENSG00000182791 ∙ NCBI:55231 ∙ ∙ HGNC:25579 ∙ Uniprot:Q9NVE4 ∙ 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 CCDC87 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC87 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				1		1
missense			79	3		82
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	79	4	0

Variants in CCDC87

This is a list of pathogenic ClinVar variants found in the CCDC87 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66590517-C-T			Likely benign (Jan 01, 2023)
11-66590536-C-T		not specified	Uncertain significance (Sep 01, 2021)
11-66590542-C-T		not specified	Uncertain significance (May 24, 2024)
11-66590545-C-T		not specified	Uncertain significance (Apr 22, 2022)
11-66590563-T-C		not specified	Uncertain significance (Sep 12, 2023)
11-66590579-T-C		not specified	Uncertain significance (May 04, 2022)
11-66590624-C-G		not specified	Uncertain significance (Dec 24, 2024)
11-66590677-T-G		not specified	Uncertain significance (Jan 10, 2025)
11-66590687-T-G		not specified	Uncertain significance (May 13, 2024)
11-66590710-C-T		not specified	Uncertain significance (Apr 19, 2023)
11-66590753-T-C		not specified	Uncertain significance (Sep 03, 2024)
11-66590767-C-T		not specified	Uncertain significance (Aug 16, 2021)
11-66590848-C-T		not specified	Likely benign (Dec 27, 2023)
11-66590917-T-C		not specified	Uncertain significance (Jun 21, 2022)
11-66590921-C-T		not specified	Uncertain significance (Oct 18, 2021)
11-66591011-G-A		not specified	Uncertain significance (Jul 30, 2024)
11-66591092-C-G		not specified	Uncertain significance (Sep 26, 2024)
11-66591182-T-C		not specified	Uncertain significance (Dec 15, 2023)
11-66591187-T-G		not specified	Uncertain significance (Jan 18, 2025)
11-66591194-A-C		not specified	Uncertain significance (Oct 22, 2021)
11-66591202-T-C		not specified	Uncertain significance (Aug 02, 2021)
11-66591313-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-66591349-A-G		not specified	Uncertain significance (Jan 01, 2025)
11-66591356-T-G		not specified	Uncertain significance (May 06, 2024)
11-66591379-A-C		not specified	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC87	protein_coding	protein_coding	ENST00000333861	1	2915

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.51e-14	0.0220	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0177	469	468	1.00	0.0000265	5469
Missense in Polyphen		109	108.77	1.0021		1294
Synonymous	0.740	189	202	0.934	0.0000109	1799
Loss of Function	0.103	21	21.5	0.976	9.35e-7	277

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: Plays a role in spermatogenesis, where it is important for normal sperm head morphology. Also required for the acrosome reaction and thus normal male fertility. {ECO:0000250|UniProtKB:Q8CDL9}.

Recessive Scores

• pRec: 0.0892

Intolerance Scores

• loftool: 0.896
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.43

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.405

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc87

Gene ontology

• Biological process: spermatogenesis;single fertilization;cell differentiation;positive regulation of fertilization;positive regulation of acrosome reaction
• Molecular function: protein binding