CCDC148

coiled-coil domain containing 148

Basic information

Region (hg38): 2:158171072-158456753

Links

ENSG00000153237 ∙ NCBI:130940 ∙ ∙ HGNC:25191 ∙ Uniprot:Q8NFR7 ∙ 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 CCDC148 gene.

• not provided (12 variants)
• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC148 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	4
missense			9	4	4	17
nonsense						0
start loss				1		1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	9	8	6

Variants in CCDC148

This is a list of pathogenic ClinVar variants found in the CCDC148 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-158172198-G-T		not specified	Uncertain significance (May 11, 2022)
2-158172209-T-C			Likely benign (Nov 27, 2018)
2-158176528-T-C		not specified	Uncertain significance (Sep 20, 2023)
2-158176536-T-C			Likely benign (Oct 09, 2018)
2-158176586-C-T			Benign (Dec 05, 2018)
2-158176610-C-T		not specified	Uncertain significance (Oct 12, 2021)
2-158176670-G-A			Likely benign (Jul 31, 2018)
2-158220601-C-G		not specified	Uncertain significance (Dec 22, 2023)
2-158250862-T-C			Benign (Dec 31, 2019)
2-158250873-G-A			Benign (Nov 19, 2018)
2-158309512-C-A		not specified	Uncertain significance (Jan 24, 2024)
2-158309512-C-G		not specified	Uncertain significance (Sep 23, 2023)
2-158309585-T-C			Likely benign (Nov 19, 2018)
2-158309623-T-A			Benign (Dec 31, 2019)
2-158313765-C-A		not specified	Uncertain significance (Dec 30, 2023)
2-158313773-T-C		not specified	Uncertain significance (Feb 05, 2024)
2-158313790-T-C		not specified	Uncertain significance (May 27, 2022)
2-158313795-C-T		not specified	Uncertain significance (Jan 23, 2024)
2-158338756-T-A		not specified	Uncertain significance (Mar 21, 2022)
2-158338873-G-A		not specified	Likely benign (Aug 09, 2021)
2-158338881-C-G		not specified	Uncertain significance (Dec 16, 2021)
2-158338906-A-T		not specified	Uncertain significance (Jan 16, 2024)
2-158340277-G-T			Likely benign (Aug 01, 2022)
2-158340336-T-C			Benign (Dec 31, 2019)
2-158340361-G-C		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC148	protein_coding	protein_coding	ENST00000283233	14	285673

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.56e-30	0.00000490	125586	0	157	125743	0.000624

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.744	319	284	1.12	0.0000137	3915
Missense in Polyphen		67	61.143	1.0958		758
Synonymous	-1.69	114	93.2	1.22	0.00000435	962
Loss of Function	-0.939	42	35.9	1.17	0.00000167	481

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00138	0.00136
Ashkenazi Jewish	0.00169	0.00169
East Asian	0.000451	0.000435
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000664	0.000642
Middle Eastern	0.000451	0.000435
South Asian	0.000789	0.000784
Other	0.000707	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.989
• rvis_EVS: 1
• rvis_percentile_EVS: 90.72

Haploinsufficiency Scores

• pHI: 0.0945
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0899

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc148

Gene ontology

• Molecular function: protein binding