CCDC138

coiled-coil domain containing 138

Basic information

Region (hg38): 2:108786757-108885477

Links

ENSG00000163006 ∙ NCBI:165055 ∙ ∙ HGNC:26531 ∙ Uniprot:Q96M89 ∙ 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 CCDC138 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC138 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			36	2		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	3	0

Variants in CCDC138

This is a list of pathogenic ClinVar variants found in the CCDC138 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-108786833-G-T		not specified	Uncertain significance (Aug 31, 2022)
2-108786835-G-C		not specified	Uncertain significance (Mar 06, 2023)
2-108786843-G-C		not specified	Uncertain significance (May 14, 2024)
2-108786895-G-T		not specified	Uncertain significance (Nov 02, 2021)
2-108788063-A-G		not specified	Likely benign (Feb 27, 2024)
2-108788856-T-A		not specified	Uncertain significance (May 30, 2024)
2-108788876-A-T		not specified	Uncertain significance (Jul 06, 2021)
2-108788914-A-G		not specified	Uncertain significance (Aug 17, 2021)
2-108788938-A-C		not specified	Uncertain significance (Jan 26, 2022)
2-108791699-C-G		not specified	Uncertain significance (Mar 23, 2022)
2-108791765-G-A			Likely benign (Jul 01, 2022)
2-108794554-A-G		not specified	Uncertain significance (Nov 10, 2023)
2-108794560-A-G		not specified	Likely benign (Apr 24, 2024)
2-108794575-C-T		not specified	Likely benign (May 14, 2024)
2-108794653-C-T		not specified	Uncertain significance (Jun 30, 2022)
2-108794662-C-T		not specified	Uncertain significance (Apr 16, 2024)
2-108798458-G-A		not specified	Uncertain significance (Dec 12, 2023)
2-108798467-C-A		not specified	Uncertain significance (May 31, 2023)
2-108798480-G-A		not specified	Uncertain significance (Sep 30, 2021)
2-108798501-A-G		not specified	Uncertain significance (Jan 26, 2023)
2-108798557-G-T		not specified	Uncertain significance (Jan 05, 2022)
2-108798564-C-A		not specified	Uncertain significance (Apr 04, 2023)
2-108798581-A-G		not specified	Uncertain significance (May 20, 2024)
2-108798582-A-G		not specified	Uncertain significance (Feb 05, 2024)
2-108804896-A-G		not specified	Uncertain significance (Oct 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC138	protein_coding	protein_coding	ENST00000295124	15	98721

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.47e-11	0.913	125625	1	122	125748	0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.208	335	324	1.03	0.0000158	4375
Missense in Polyphen		16	13.568	1.1793		176
Synonymous	-0.907	131	118	1.11	0.00000604	1189
Loss of Function	1.96	22	34.4	0.640	0.00000160	467

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000931	0.000929
Ashkenazi Jewish	0.00	0.00
East Asian	0.000276	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000421	0.000404
Middle Eastern	0.000276	0.000272
South Asian	0.00154	0.00144
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.325
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.57

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.328
• ghis: 0.622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0481

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc138