CCDC144NL

CCDC144A N-terminal pseudogene

Basic information

Region (hg38): 17:20893392-20896020

Links

ENSG00000205212 ∙ NCBI:339184 ∙ ∙ HGNC:33735 ∙ Uniprot:Q6NUI1 ∙ 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 CCDC144NL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC144NL 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				4	6	10
Total	0	0	0	4	6

Variants in CCDC144NL

This is a list of pathogenic ClinVar variants found in the CCDC144NL region.

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

Position	Type	Phenotype	Significance	ClinVar
17-20895774-C-T			Likely benign (Feb 01, 2023)
17-20895790-G-A			Likely benign (Dec 31, 2019)
17-20895806-A-G			Benign (Dec 31, 2019)
17-20895813-C-T			Benign (Jan 30, 2018)
17-20895898-C-T			Benign (Dec 31, 2019)
17-20895905-T-C			Likely benign (Mar 05, 2018)
17-20895923-T-C			Benign (Apr 10, 2018)
17-20895979-C-A			Likely benign (Feb 01, 2023)
17-20895994-C-T			Benign (Apr 10, 2018)
17-20895995-C-T			Benign (Apr 10, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC144NL	protein_coding	protein_coding	ENST00000327925	4	59694

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.05e-14	0.00146	125445	1	145	125591	0.000581

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.19	236	133	1.78	0.00000798	1406
Missense in Polyphen		67	32.71	2.0483		363
Synonymous	-4.01	93	55.1	1.69	0.00000407	417
Loss of Function	-2.06	16	9.25	1.73	3.94e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00117	0.00116
Ashkenazi Jewish	0.00361	0.00348
East Asian	0.000817	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.000439	0.000432
Middle Eastern	0.000817	0.000816
South Asian	0.000400	0.000392
Other	0.000496	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.940
• rvis_EVS: 1.27
• rvis_percentile_EVS: 93.6

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.278

Gene Damage Prediction

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