CCDC57

coiled-coil domain containing 57

Basic information

Region (hg38): 17:82101459-82212878

Links

ENSG00000176155 ∙ NCBI:284001 ∙ ∙ HGNC:27564 ∙ Uniprot:Q2TAC2 ∙ 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 CCDC57 gene.

• Inborn genetic diseases (42 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC57 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		2
missense			37	6		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	8	0

Variants in CCDC57

This is a list of pathogenic ClinVar variants found in the CCDC57 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-82101689-A-G		not specified	Uncertain significance (Mar 14, 2023)
17-82101721-C-A		not specified	Uncertain significance (May 17, 2023)
17-82101752-C-T		not specified	Uncertain significance (Jul 20, 2021)
17-82101794-T-G		not specified	Uncertain significance (Oct 26, 2022)
17-82101841-G-T		not specified	Uncertain significance (Apr 28, 2022)
17-82127820-G-C		not specified	Uncertain significance (Apr 20, 2023)
17-82127838-G-C		not specified	Likely benign (Jan 31, 2022)
17-82128509-G-T		not specified	Uncertain significance (May 23, 2023)
17-82128566-G-A		not specified	Uncertain significance (Mar 04, 2024)
17-82128594-C-T		not specified	Uncertain significance (Aug 16, 2021)
17-82157888-G-C		not specified	Uncertain significance (Jul 05, 2023)
17-82157900-G-C		not specified	Uncertain significance (Feb 17, 2022)
17-82157921-C-T		not specified	Likely benign (Oct 03, 2022)
17-82157948-C-T		not specified	Uncertain significance (Apr 07, 2022)
17-82163250-C-T		not specified	Uncertain significance (Dec 12, 2023)
17-82163292-G-T		not specified	Uncertain significance (Jan 09, 2024)
17-82163303-C-T		not specified	Uncertain significance (Aug 16, 2021)
17-82163331-C-T		not specified	Uncertain significance (Jun 23, 2023)
17-82171725-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-82171744-A-T		not specified	Uncertain significance (Dec 02, 2022)
17-82171771-C-G		not specified	Uncertain significance (Jan 02, 2024)
17-82171785-G-T		not specified	Uncertain significance (Jan 02, 2024)
17-82171832-G-C			Likely benign (Sep 01, 2022)
17-82172793-C-T		not specified	Likely benign (Mar 14, 2023)
17-82178518-C-T		not specified	Likely benign (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC57	protein_coding	protein_coding	ENST00000392343	13	111371

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.50e-16	0.339	124589	0	98	124687	0.000393

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.451	421	448	0.940	0.0000283	4808
Missense in Polyphen		109	115.8	0.94127		1506
Synonymous	1.74	160	191	0.840	0.0000122	1520
Loss of Function	1.46	29	38.8	0.747	0.00000220	399

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00155	0.00155
Ashkenazi Jewish	0.00	0.00
East Asian	0.000615	0.000612
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000243	0.000239
Middle Eastern	0.000615	0.000612
South Asian	0.0000992	0.0000980
Other	0.000996	0.000990

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.170
• ghis: 0.510

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.264

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Ccdc57
• Phenotype: homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; skeleton phenotype; hematopoietic system phenotype

Gene ontology

• Molecular function: protein binding