CCDC38

coiled-coil domain containing 38

Basic information

Region (hg38): 12:95867047-95942635

Links

ENSG00000165972 ∙ NCBI:120935 ∙ ∙ HGNC:26843 ∙ Uniprot:Q502W7 ∙ 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 CCDC38 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC38 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						0
missense			40	5		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	40	5	0

Variants in CCDC38

This is a list of pathogenic ClinVar variants found in the CCDC38 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-95867122-T-C		not specified	Uncertain significance (Jun 06, 2023)
12-95867189-A-G		not specified	Likely benign (Feb 27, 2024)
12-95869485-T-C		not specified	Uncertain significance (May 31, 2023)
12-95869499-A-G		not specified	Uncertain significance (May 24, 2024)
12-95869500-C-T		not specified	Uncertain significance (Jan 16, 2024)
12-95869568-C-T		not specified	Uncertain significance (Apr 08, 2024)
12-95872262-G-A		not specified	Uncertain significance (Oct 05, 2022)
12-95872279-A-T		not specified	Uncertain significance (Jun 21, 2021)
12-95872312-A-G		not specified	Uncertain significance (May 09, 2022)
12-95872345-C-T		not specified	Uncertain significance (Oct 17, 2023)
12-95872346-G-A		not specified	Uncertain significance (Apr 01, 2024)
12-95872385-C-T		not specified	Likely benign (Oct 05, 2021)
12-95872386-G-T		not specified	Uncertain significance (Jul 20, 2021)
12-95878236-A-G		not specified	Uncertain significance (Dec 14, 2022)
12-95878246-G-T		not specified	Uncertain significance (Sep 20, 2023)
12-95878248-T-C		not specified	Likely benign (Feb 17, 2024)
12-95878269-G-A		not specified	Uncertain significance (Jan 23, 2023)
12-95878278-T-G		not specified	Uncertain significance (Apr 04, 2024)
12-95878285-C-T		not specified	Uncertain significance (Nov 07, 2023)
12-95878308-A-C		not specified	Uncertain significance (Mar 18, 2024)
12-95878309-T-C		not specified	Uncertain significance (Sep 16, 2021)
12-95878326-A-G		not specified	Uncertain significance (Apr 07, 2022)
12-95878335-A-G		not specified	Uncertain significance (Dec 19, 2022)
12-95878337-G-C		not specified	Uncertain significance (Mar 31, 2023)
12-95879653-T-C		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC38	protein_coding	protein_coding	ENST00000344280	15	75927

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.83e-13	0.353	125490	0	258	125748	0.00103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.150	275	282	0.975	0.0000141	3724
Missense in Polyphen		85	83.77	1.0147		1198
Synonymous	-0.752	107	97.6	1.10	0.00000495	975
Loss of Function	1.27	24	31.7	0.756	0.00000150	420

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000884	0.000881
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.00420	0.00409
Finnish	0.000694	0.000693
European (Non-Finnish)	0.00109	0.00108
Middle Eastern	0.00420	0.00409
South Asian	0.000528	0.000523
Other	0.00148	0.00147

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.974
• rvis_EVS: 0.45
• rvis_percentile_EVS: 77.98

Haploinsufficiency Scores

• pHI: 0.0954
• hipred: N
• hipred_score: 0.145

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.119

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc38

Gene ontology

• Cellular component: cytoplasm;centrosome