CCDC144A

coiled-coil domain containing 144A

Basic information

Region (hg38): 17:16689537-16777881

Links

ENSG00000170160 ∙ NCBI:9720 ∙ OMIM:619413 ∙ HGNC:29072 ∙ Uniprot:A2RUR9 ∙ 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 CCDC144A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC144A 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			68	11		79
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	68	12	0

Variants in CCDC144A

This is a list of pathogenic ClinVar variants found in the CCDC144A region.

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

Position	Type	Phenotype	Significance	ClinVar
17-16690498-G-A		not specified	Likely benign (Nov 29, 2023)
17-16690516-G-A		not specified	Uncertain significance (Feb 07, 2025)
17-16690531-A-G		not specified	Uncertain significance (Oct 25, 2022)
17-16690540-C-T		not specified	Uncertain significance (Nov 20, 2024)
17-16690559-G-C		not specified	Uncertain significance (Oct 09, 2024)
17-16690644-G-A		not specified	Uncertain significance (Jun 18, 2024)
17-16690692-C-A		not specified	Uncertain significance (Apr 04, 2024)
17-16705201-A-C		not specified	Uncertain significance (May 18, 2023)
17-16705202-A-G		not specified	Uncertain significance (Aug 17, 2022)
17-16705301-G-C		not specified	Uncertain significance (May 26, 2022)
17-16705307-A-T		not specified	Uncertain significance (Jul 14, 2021)
17-16705315-A-C		not specified	Uncertain significance (Jun 21, 2023)
17-16705348-C-T		not specified	Uncertain significance (Feb 23, 2023)
17-16707500-A-G			Likely benign (Mar 01, 2024)
17-16707520-G-A		not specified	Uncertain significance (Nov 11, 2024)
17-16708812-C-A		not specified	Uncertain significance (Sep 16, 2021)
17-16708819-G-A		not specified	Uncertain significance (Aug 10, 2021)
17-16708830-G-A		not specified	Uncertain significance (Jul 09, 2024)
17-16708832-G-A		not specified	Uncertain significance (Oct 05, 2021)
17-16708848-C-G		not specified	Uncertain significance (Feb 26, 2024)
17-16708850-A-G		not specified	Likely benign (Mar 29, 2024)
17-16708868-C-T		not specified	Uncertain significance (Dec 27, 2022)
17-16708879-A-T		not specified	Uncertain significance (Aug 28, 2024)
17-16708937-G-A		not specified	Likely benign (Dec 06, 2021)
17-16709087-T-C		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC144A	protein_coding	protein_coding	ENST00000443444	18	114917

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.76e-14	0.996	125531	0	57	125588	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.02	415	548	0.757	0.0000275	9478
Missense in Polyphen		36	53.391	0.67427		961
Synonymous	0.962	188	206	0.915	0.0000116	2427
Loss of Function	2.81	30	51.8	0.579	0.00000245	909

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000344	0.000343
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000492	0.0000462
European (Non-Finnish)	0.000430	0.000379
Middle Eastern	0.00	0.00
South Asian	0.000233	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0164
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.227

Gene Damage Prediction

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