CCDC149

coiled-coil domain containing 149

Basic information

Region (hg38): 4:24803514-24980204

Links

ENSG00000181982 ∙ NCBI:91050 ∙ ∙ HGNC:25405 ∙ Uniprot:Q6ZUS6 ∙ 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 CCDC149 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC149 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			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	27	2	0

Variants in CCDC149

This is a list of pathogenic ClinVar variants found in the CCDC149 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-24808400-C-A		not specified	Uncertain significance (Dec 21, 2022)
4-24808469-G-A		not specified	Uncertain significance (Nov 22, 2023)
4-24808501-T-G		not specified	Uncertain significance (Apr 25, 2022)
4-24808583-T-C		not specified	Uncertain significance (Jan 02, 2024)
4-24808695-C-G		not specified	Uncertain significance (Jan 10, 2022)
4-24808711-C-G		not specified	Uncertain significance (Dec 02, 2021)
4-24808711-C-T		not specified	Likely benign (Jan 04, 2024)
4-24808739-C-T		not specified	Uncertain significance (May 26, 2023)
4-24808762-G-A		not specified	Uncertain significance (Jul 22, 2022)
4-24808771-G-A		not specified	Likely benign (Feb 27, 2024)
4-24819861-T-C		not specified	Uncertain significance (Jan 31, 2024)
4-24819895-C-G		not specified	Uncertain significance (Nov 01, 2022)
4-24819898-C-T		not specified	Uncertain significance (Jun 21, 2023)
4-24819901-A-T		not specified	Uncertain significance (Sep 12, 2023)
4-24822569-G-C		not specified	Uncertain significance (May 01, 2022)
4-24831524-T-C		not specified	Uncertain significance (May 04, 2023)
4-24831534-C-A		not specified	Uncertain significance (Nov 18, 2023)
4-24831546-C-T		not specified	Uncertain significance (May 28, 2024)
4-24835007-G-C		not specified	Uncertain significance (Mar 16, 2022)
4-24835032-T-C		not specified	Uncertain significance (Jun 30, 2023)
4-24837336-C-T		not specified	Uncertain significance (Aug 19, 2021)
4-24838182-G-T		not specified	Uncertain significance (Jul 06, 2021)
4-24838193-T-G		not specified	Uncertain significance (Apr 23, 2024)
4-24838200-C-T		not specified	Uncertain significance (Aug 08, 2022)
4-24838239-C-T		not specified	Uncertain significance (May 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC149	protein_coding	protein_coding	ENST00000504487	12	174088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000190	0.995	125720	0	26	125746	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	214	268	0.797	0.0000149	3454
Missense in Polyphen		69	102.34	0.6742		1239
Synonymous	0.574	104	112	0.931	0.00000684	1021
Loss of Function	2.47	12	25.4	0.472	0.00000142	291

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000450	0.000449
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0980

Intolerance Scores

• loftool: 0.135
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.160
• hipred: N
• hipred_score: 0.378
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.382

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc149