CCDC102B

coiled-coil domain containing 102B

Basic information

Region (hg38): 18:68715208-69055189

Previous symbols: [ "C18orf14", "ACY1L" ]

Links

ENSG00000150636 ∙ NCBI:79839 ∙ ∙ HGNC:26295 ∙ Uniprot:Q68D86 ∙ 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 CCDC102B gene.

• Inborn genetic diseases (22 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC102B 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			19	3	4	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	5	5

Variants in CCDC102B

This is a list of pathogenic ClinVar variants found in the CCDC102B region.

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

Position	Type	Phenotype	Significance	ClinVar
18-68715237-T-C			Benign (Nov 12, 2018)
18-68715260-G-A			Benign (May 25, 2021)
18-68836786-G-A		not specified	Uncertain significance (Nov 29, 2021)
18-68836840-G-A		not specified	Likely benign (Mar 21, 2023)
18-68836841-C-T			Benign (Jun 18, 2018)
18-68836845-G-A		not specified	Uncertain significance (Nov 08, 2022)
18-68836881-T-C		not specified	Uncertain significance (Oct 03, 2022)
18-68836945-C-T		not specified	Uncertain significance (Aug 21, 2023)
18-68836970-T-C			Likely benign (Jul 01, 2022)
18-68836971-T-C		not specified	Uncertain significance (Feb 28, 2024)
18-68836983-C-T		not specified	Uncertain significance (Dec 08, 2023)
18-68837017-C-G		not specified	Uncertain significance (Nov 15, 2021)
18-68837035-C-G		not specified	Uncertain significance (Jul 14, 2023)
18-68837097-G-A		not specified	Uncertain significance (Oct 16, 2023)
18-68837259-G-A		not specified	Uncertain significance (Dec 14, 2023)
18-68837274-A-G		not specified	Uncertain significance (Dec 14, 2023)
18-68837323-A-G		not specified	Likely benign (Nov 28, 2023)
18-68837347-C-T		not specified	Uncertain significance (Dec 16, 2023)
18-68838718-G-T		not specified	Uncertain significance (Dec 17, 2023)
18-68838750-G-A		not specified	Uncertain significance (Sep 22, 2022)
18-68838754-C-A		not specified	Uncertain significance (Dec 12, 2023)
18-68838809-C-G			Benign (Oct 09, 2017)
18-68838809-C-T		not specified	Likely benign (Dec 21, 2023)
18-68838829-A-G		not specified	Uncertain significance (Jan 26, 2022)
18-68838844-C-T		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC102B	protein_coding	protein_coding	ENST00000360242	7	339981

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.22e-16	0.0191	125280	1	467	125748	0.00186

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.551	280	255	1.10	0.0000129	3384
Missense in Polyphen		67	56.09	1.1945		833
Synonymous	0.747	82	91.1	0.900	0.00000442	881
Loss of Function	0.354	25	27.0	0.927	0.00000146	331

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00213	0.00209
Ashkenazi Jewish	0.00	0.00
East Asian	0.000935	0.000925
Finnish	0.00333	0.00329
European (Non-Finnish)	0.00284	0.00268
Middle Eastern	0.000935	0.000925
South Asian	0.000531	0.000523
Other	0.00214	0.00196

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0854

Intolerance Scores

• loftool: 0.958
• rvis_EVS: 1.82
• rvis_percentile_EVS: 97.02

Haploinsufficiency Scores

• pHI: 0.717
• hipred: N
• hipred_score: 0.123
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0584

Gene Damage Prediction

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

Gene ontology

• Molecular function: protein binding