CCDC47

coiled-coil domain containing 47

Basic information

Region (hg38): 17:63745255-63776351

Links

ENSG00000108588 ∙ NCBI:57003 ∙ OMIM:618260 ∙ HGNC:24856 ∙ Uniprot:Q96A33 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• trichohepatoneurodevelopmental syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Trichohepatoneurodevelopmental syndrome	AR	Allergy/Immunology/Infectious	Among other findings, individuals have been described with susceptibility to infections, and antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious; Craniofacial; Dental; Dermatologic; Gastrointestinal; Musculoskeletal; Neurologic	30401460

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC47 gene.

• Trichohepatoneurodevelopmental syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC47 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			21			21
nonsense		3				3
start loss						0
frameshift	1	3				4
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1	1	3
non coding				1	3	4
Total	1	6	21	1	4

Variants in CCDC47

This is a list of pathogenic ClinVar variants found in the CCDC47 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-63746945-C-T		not specified	Uncertain significance (Sep 22, 2023)
17-63751952-C-T		CCDC47-related disorder	Benign (Feb 26, 2020)
17-63752005-T-C		not specified	Uncertain significance (Mar 01, 2023)
17-63752014-G-A		not specified	Uncertain significance (Jul 27, 2024)
17-63752078-G-GGCACGGTTCTTATCTGCTTTTT		Trichohepatoneurodevelopmental syndrome	Likely pathogenic (Mar 22, 2022)
17-63752334-G-A		Trichohepatoneurodevelopmental syndrome • Global developmental delay with dysmorphic features, liver dysfunction, pruritus, and woolly hair	Pathogenic/Likely pathogenic (Jan 01, 2023)
17-63752357-GA-G		Global developmental delay with dysmorphic features, liver dysfunction, pruritus, and woolly hair • Trichohepatoneurodevelopmental syndrome	Likely pathogenic (Sep 24, 2018)
17-63752377-CA-C		Trichohepatoneurodevelopmental syndrome • Global developmental delay with dysmorphic features, liver dysfunction, pruritus, and woolly hair	Likely pathogenic (Sep 24, 2018)
17-63752390-G-C		not specified	Uncertain significance (Dec 21, 2022)
17-63752408-T-C		not specified	Uncertain significance (Nov 01, 2021)
17-63752432-G-A		CCDC47-related disorder	Benign (Jun 11, 2018)
17-63752629-C-T		Trichohepatoneurodevelopmental syndrome	Benign (Jul 14, 2021)
17-63752756-A-G		CCDC47-related disorder	Likely benign (Feb 22, 2019)
17-63752765-T-C		not specified	Uncertain significance (Oct 25, 2024)
17-63752777-G-A		not specified	Uncertain significance (Nov 10, 2022)
17-63754439-A-T		not specified	Uncertain significance (Jun 06, 2023)
17-63754485-T-C		not specified	Uncertain significance (Apr 19, 2024)
17-63754488-T-G		not specified	Uncertain significance (Jul 05, 2023)
17-63756231-C-T		CCDC47-related disorder	Likely benign (Jan 08, 2020)
17-63756277-T-G		not specified	Uncertain significance (Jun 01, 2023)
17-63756292-A-G		CCDC47-related disorder	Uncertain significance (Sep 14, 2022)
17-63756301-G-A		not specified	Uncertain significance (Aug 04, 2023)
17-63756302-G-A		not specified	Uncertain significance (Jun 22, 2023)
17-63756310-T-A		not specified	Uncertain significance (Aug 14, 2024)
17-63756495-G-A		Trichohepatoneurodevelopmental syndrome • Global developmental delay with dysmorphic features, liver dysfunction, pruritus, and woolly hair	Likely pathogenic (Sep 24, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC47	protein_coding	protein_coding	ENST00000225726	12	31102

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.13e-8	0.968	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	212	259	0.818	0.0000133	3249
Missense in Polyphen		66	85.422	0.77263		1023
Synonymous	0.158	85	86.9	0.979	0.00000418	831
Loss of Function	2.07	16	27.8	0.576	0.00000159	323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000118	0.000118
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000218	0.000217
South Asian	0.000362	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.286
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.16

Haploinsufficiency Scores

• pHI: 0.466
• hipred: N
• hipred_score: 0.426
• ghis: 0.620

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.910

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc47
• Phenotype: cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: osteoblast differentiation;ER overload response;endoplasmic reticulum organization;post-embryonic development;ubiquitin-dependent ERAD pathway;calcium ion homeostasis
• Cellular component: endoplasmic reticulum;rough endoplasmic reticulum;membrane;integral component of membrane
• Molecular function: RNA binding;calcium ion binding;protein binding