CCDC190

coiled-coil domain containing 190

Basic information

Region (hg38): 1:162824457-162868761

Previous symbols: [ "C1orf110" ]

Links

ENSG00000185860 ∙ NCBI:339512 ∙ ∙ HGNC:28736 ∙ Uniprot:Q86UF4 ∙ 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 CCDC190 gene.

• Inborn genetic diseases (14 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC190 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in CCDC190

This is a list of pathogenic ClinVar variants found in the CCDC190 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-162854784-G-T		not specified	Uncertain significance (Jan 04, 2022)
1-162854803-A-G		not specified	Uncertain significance (Nov 09, 2023)
1-162854826-G-A		not specified	Likely benign (Aug 02, 2022)
1-162854830-A-C		not specified	Uncertain significance (Dec 22, 2023)
1-162854880-G-C		not specified	Uncertain significance (Oct 03, 2022)
1-162854896-G-C		not specified	Uncertain significance (Jun 24, 2022)
1-162855016-C-T		not specified	Uncertain significance (Dec 16, 2022)
1-162855109-T-C		not specified	Uncertain significance (Mar 07, 2024)
1-162855162-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-162855166-C-A		not specified	Uncertain significance (Mar 07, 2023)
1-162855210-G-A		not specified	Uncertain significance (Aug 16, 2021)
1-162855272-C-T		not specified	Uncertain significance (May 05, 2023)
1-162855328-A-T		not specified	Uncertain significance (Mar 29, 2022)
1-162855352-C-T		not specified	Uncertain significance (Aug 14, 2023)
1-162855696-C-T		not specified	Uncertain significance (Jan 02, 2024)
1-162855737-A-G		not specified	Uncertain significance (Aug 02, 2022)
1-162859531-C-G		not specified	Uncertain significance (Jul 14, 2021)
1-162859552-A-G		not specified	Uncertain significance (May 09, 2023)
1-162859559-G-A			not provided (-)
1-162859577-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-162859613-T-C		not specified	Uncertain significance (Sep 01, 2021)
1-162859630-A-G		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC190	protein_coding	protein_coding	ENST00000367910	3	44358

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00411	0.672	124535	1	75	124611	0.000305

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.160	149	155	0.964	0.00000734	1993
Missense in Polyphen		34	44.565	0.76292		632
Synonymous	-0.763	64	56.7	1.13	0.00000270	560
Loss of Function	0.614	4	5.56	0.719	2.34e-7	74

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.000398	0.000398
East Asian	0.000112	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000125	0.000124
Middle Eastern	0.000112	0.000111
South Asian	0.00164	0.00160
Other	0.000331	0.000331

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.82

Haploinsufficiency Scores

• pHI: 0.00869
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Ccdc190