CCDC140

CCDC140 long non-coding RNA, the group of Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 2:222298147-222305217

Links

ENSG00000163081 ∙ NCBI:151278 ∙ ∙ HGNC:26514 ∙ Uniprot:Q96MF4 ∙ 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 CCDC140 gene.

• not provided (3 variants)
• Waardenburg syndrome type 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC140 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	2	11	5	3	25
Total	4	2	11	5	3

Variants in CCDC140

This is a list of pathogenic ClinVar variants found in the CCDC140 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-222298513-G-C			Likely benign (Dec 30, 2023)
2-222298528-T-TA			Likely pathogenic (May 16, 2016)
2-222298539-G-A			Uncertain significance (Jan 25, 2023)
2-222298545-C-A			Likely benign (Sep 05, 2023)
2-222298547-G-A			Likely benign (Jul 28, 2023)
2-222298547-GC-G			Pathogenic (Jun 28, 2018)
2-222298550-AC-A		Waardenburg syndrome type 1	Pathogenic (Jan 09, 2025)
2-222298552-G-T			Uncertain significance (Nov 01, 2021)
2-222298553-C-T			Likely benign (Oct 18, 2023)
2-222298562-C-G		Inborn genetic diseases	Uncertain significance (Jul 27, 2024)
2-222298564-G-A			Pathogenic (Jan 30, 2024)
2-222298569-G-A		Waardenburg syndrome • Craniofacial-deafness-hand syndrome	Uncertain significance (Feb 01, 2021)
2-222298570-G-A			Uncertain significance (Jan 09, 2024)
2-222298576-GC-G			Pathogenic (May 16, 2018)
2-222298597-C-A			Uncertain significance (Aug 18, 2023)
2-222298600-C-G			Uncertain significance (Apr 29, 2024)
2-222298607-C-T		not specified	Likely benign (Nov 05, 2024)
2-222298699-T-C		Waardenburg syndrome type 1	Likely pathogenic (Jan 09, 2025)
2-222298714-G-A		Waardenburg syndrome • Craniofacial-deafness-hand syndrome	Uncertain significance (Jan 13, 2018)
2-222298771-G-A		Craniofacial-deafness-hand syndrome • Waardenburg syndrome	Uncertain significance (Jan 13, 2018)
2-222298771-G-T		Waardenburg syndrome • Craniofacial-deafness-hand syndrome	Uncertain significance (Jan 13, 2018)
2-222298820-G-A		Waardenburg syndrome • Craniofacial-deafness-hand syndrome	Benign (Jan 13, 2018)
2-222298863-T-G		Craniofacial-deafness-hand syndrome • Waardenburg syndrome	Uncertain significance (Jan 13, 2018)
2-222298974-C-A		Waardenburg syndrome • Craniofacial-deafness-hand syndrome	Benign (Jan 12, 2018)
2-222299309-G-C			Benign (Apr 09, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC140	protein_coding	protein_coding	ENST00000295226	1	7071

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.33	125	89.6	1.39	0.00000395	1049
Missense in Polyphen		20	8.1721	2.4474		77
Synonymous	-0.843	43	36.5	1.18	0.00000166	336
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.554
• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.95

Haploinsufficiency Scores

• pHI: 0.0462
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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