CCDC74B

coiled-coil domain containing 74B

Basic information

Region (hg38): 2:130139287-130145134

Links

ENSG00000152076 ∙ NCBI:91409 ∙ ∙ HGNC:25267 ∙ Uniprot:Q96LY2 ∙ 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 CCDC74B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC74B 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			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7	1		8
Total	0	0	32	4	0

Variants in CCDC74B

This is a list of pathogenic ClinVar variants found in the CCDC74B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-130139565-G-A		not specified	Uncertain significance (Feb 23, 2023)
2-130139568-C-T		not specified	Uncertain significance (Dec 26, 2023)
2-130139569-G-A		not specified	Uncertain significance (Apr 30, 2024)
2-130139577-C-T		not specified	Uncertain significance (Dec 18, 2023)
2-130139613-T-A		not specified	Uncertain significance (Feb 12, 2024)
2-130139636-C-A		not specified	Uncertain significance (Oct 06, 2023)
2-130139638-G-T		not specified	Uncertain significance (Mar 17, 2023)
2-130139670-A-G		not specified	Uncertain significance (Feb 26, 2024)
2-130139678-G-C		not specified	Uncertain significance (Apr 09, 2024)
2-130139900-G-A		not specified	Uncertain significance (Dec 13, 2023)
2-130139909-T-C		not specified	Uncertain significance (Jan 30, 2024)
2-130140087-G-A			Likely benign (Mar 01, 2023)
2-130140188-C-G		not specified	Uncertain significance (May 30, 2023)
2-130140237-C-A		not specified	Uncertain significance (Dec 19, 2022)
2-130140277-T-C		not specified	Uncertain significance (Jun 17, 2024)
2-130140291-G-A		not specified	Uncertain significance (Oct 28, 2023)
2-130140291-G-C		not specified	Likely benign (Dec 03, 2021)
2-130140303-T-C		not specified	Uncertain significance (Oct 13, 2023)
2-130140351-G-C		not specified	Uncertain significance (Feb 26, 2024)
2-130141174-C-T		not specified	Uncertain significance (Jun 16, 2023)
2-130141194-T-G		not specified	Uncertain significance (Jun 18, 2021)
2-130141230-G-A		not specified	Uncertain significance (Jul 05, 2023)
2-130141239-G-A		not specified	Uncertain significance (Nov 12, 2021)
2-130142157-A-T		not specified	Uncertain significance (Oct 04, 2022)
2-130142205-C-T		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC74B	protein_coding	protein_coding	ENST00000310463	8	5848

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.24e-10	0.0990	125079	4	664	125747	0.00266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.666	250	222	1.13	0.0000128	2402
Missense in Polyphen		92	72.637	1.2666		899
Synonymous	-1.44	117	98.8	1.18	0.00000620	779
Loss of Function	0.289	16	17.3	0.925	8.22e-7	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0172	0.0172
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000587	0.000580
Middle Eastern	0.000109	0.000109
South Asian	0.000327	0.000294
Other	0.00296	0.00294

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.973
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.54

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.173

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc74a