CCDC85A

coiled-coil domain containing 85A

Basic information

Region (hg38): 2:56183989-56386172

Links

ENSG00000055813 ∙ NCBI:114800 ∙ ∙ HGNC:29400 ∙ Uniprot:Q96PX6 ∙ 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 CCDC85A gene.

• Inborn genetic diseases (21 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC85A 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in CCDC85A

This is a list of pathogenic ClinVar variants found in the CCDC85A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-56184629-C-G		not specified	Uncertain significance (Dec 14, 2023)
2-56184662-C-T		not specified	Uncertain significance (May 08, 2023)
2-56184671-A-G		not specified	Uncertain significance (Oct 03, 2022)
2-56184685-G-T		not specified	Uncertain significance (Jan 16, 2024)
2-56184686-C-T		not specified	Uncertain significance (May 11, 2022)
2-56184698-C-G		not specified	Uncertain significance (Feb 27, 2024)
2-56184750-G-C		not specified	Uncertain significance (Jul 20, 2021)
2-56184784-C-T		not specified	Uncertain significance (Feb 15, 2023)
2-56192487-A-T		not specified	Uncertain significance (Nov 21, 2022)
2-56192588-G-A		not specified	Uncertain significance (Feb 06, 2024)
2-56192594-T-C		not specified	Uncertain significance (Oct 25, 2022)
2-56192624-G-T		not specified	Uncertain significance (Aug 17, 2022)
2-56192774-A-G		not specified	Uncertain significance (Oct 26, 2022)
2-56192786-C-G		not specified	Uncertain significance (Jan 08, 2024)
2-56192801-G-C		not specified	Uncertain significance (Dec 13, 2023)
2-56192901-C-T		not specified	Uncertain significance (Oct 05, 2023)
2-56192968-C-T			Likely benign (Mar 01, 2022)
2-56192969-G-A		not specified	Uncertain significance (Jan 04, 2024)
2-56192973-A-G		not specified	Uncertain significance (Jun 24, 2022)
2-56193011-C-A		not specified	Uncertain significance (Feb 13, 2024)
2-56193023-A-G		not specified	Uncertain significance (May 27, 2022)
2-56193068-C-T		not specified	Uncertain significance (Feb 22, 2023)
2-56193120-A-T		not specified	Uncertain significance (Feb 13, 2023)
2-56193189-G-C		not specified	Uncertain significance (Aug 22, 2023)
2-56193192-A-G		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC85A	protein_coding	protein_coding	ENST00000407595	6	202051

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000154	0.967	124675	0	24	124699	0.0000962

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.214	326	315	1.03	0.0000183	3569
Missense in Polyphen		135	144.6	0.93363		1645
Synonymous	-2.20	165	133	1.24	0.00000848	1095
Loss of Function	1.95	11	20.5	0.536	0.00000103	250

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000279	0.000269
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000186	0.000186
European (Non-Finnish)	0.0000926	0.0000884
Middle Eastern	0.00	0.00
South Asian	0.0000667	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0944

Intolerance Scores

• loftool: 0.326
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.300
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.280

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc85a