CCDC150

coiled-coil domain containing 150

Basic information

Region (hg38): 2:196639553-196763490

Links

ENSG00000144395 ∙ NCBI:284992 ∙ ∙ HGNC:26834 ∙ Uniprot:Q8NCX0 ∙ 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 CCDC150 gene.

• Inborn genetic diseases (39 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC150 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			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	2	0

Variants in CCDC150

This is a list of pathogenic ClinVar variants found in the CCDC150 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-196639771-A-T		not specified	Uncertain significance (Aug 28, 2023)
2-196646369-C-T		not specified	Uncertain significance (May 26, 2022)
2-196646371-G-A		not specified	Uncertain significance (Sep 26, 2023)
2-196646372-T-C		not specified	Uncertain significance (Dec 28, 2023)
2-196656634-G-T		not specified	Uncertain significance (Feb 28, 2024)
2-196656691-C-T		not specified	Uncertain significance (Aug 11, 2022)
2-196656713-G-A		not specified	Uncertain significance (Aug 16, 2022)
2-196656744-C-A		not specified	Uncertain significance (Aug 09, 2021)
2-196656826-G-A		not specified	Uncertain significance (Nov 29, 2023)
2-196656827-A-G		not specified	Uncertain significance (Nov 10, 2022)
2-196657075-A-G		not specified	Uncertain significance (May 13, 2022)
2-196657093-T-G		not specified	Uncertain significance (Feb 07, 2023)
2-196657107-G-T		not specified	Uncertain significance (Jun 01, 2023)
2-196657110-A-G		not specified	Uncertain significance (May 26, 2022)
2-196658804-A-G		not specified	Uncertain significance (Jan 31, 2024)
2-196658826-C-G		not specified	Uncertain significance (May 18, 2022)
2-196665678-A-C		not specified	Uncertain significance (Dec 06, 2022)
2-196666753-G-A		not specified	Likely benign (May 25, 2022)
2-196666794-CA-C		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)
2-196666794-C-CA		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)
2-196666797-A-C		not specified	Likely benign (Oct 13, 2023)
2-196666818-A-C		not specified	Uncertain significance (Sep 20, 2023)
2-196666837-A-C		not specified	Uncertain significance (Mar 28, 2023)
2-196672429-A-G		not specified	Uncertain significance (Oct 14, 2023)
2-196674283-T-G		not specified	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC150	protein_coding	protein_coding	ENST00000389175	28	123937

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.95e-37	0.0000666	121801	20	2816	124637	0.0114

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.146	521	530	0.982	0.0000270	7286
Missense in Polyphen		135	153.12	0.88166		2232
Synonymous	-1.12	201	182	1.11	0.00000879	1871
Loss of Function	0.707	59	65.2	0.905	0.00000340	813

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00890	0.00889
Ashkenazi Jewish	0.00977	0.00979
East Asian	0.00327	0.00323
Finnish	0.00348	0.00349
European (Non-Finnish)	0.0160	0.0159
Middle Eastern	0.00327	0.00323
South Asian	0.0165	0.0164
Other	0.0139	0.0140

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.985
• rvis_EVS: 0.16
• rvis_percentile_EVS: 64.97

Haploinsufficiency Scores

• pHI: 0.186
• hipred: N
• hipred_score: 0.144
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.113

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc150

Gene ontology

• Molecular function: protein binding