CCDC174

coiled-coil domain containing 174

Basic information

Region (hg38): 3:14651762-14672659

Previous symbols: [ "C3orf19" ]

Links

ENSG00000154781 ∙ NCBI:51244 ∙ OMIM:616735 ∙ HGNC:28033 ∙ Uniprot:Q6PII3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• severe hypotonia-psychomotor developmental delay-strabismus-cardiac septal defect syndrome (Limited), mode of inheritance: AR
• severe hypotonia-psychomotor developmental delay-strabismus-cardiac septal defect syndrome (Supportive), mode of inheritance: AR
• severe hypotonia-psychomotor developmental delay-strabismus-cardiac septal defect syndrome (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypotonia, infantile, with psychomotor retardation	AR	Cardiovascular	Individuals have been described with congenital heart anomalies, and awareness may enable early diagnosis and management	Cardiovascular; Genitourinary; Musculoskeletal; Neurologic	26358778

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC174 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC174 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				9	3	12
missense			34	9	2	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				2	14	16
Total	0	0	34	20	19

Variants in CCDC174

This is a list of pathogenic ClinVar variants found in the CCDC174 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-14651855-C-G		not specified	Uncertain significance (May 27, 2022)
3-14651871-C-T		not specified	Uncertain significance (Dec 06, 2022)
3-14654426-T-G		not specified	Uncertain significance (Mar 01, 2023)
3-14654454-G-A		not specified	Uncertain significance (Mar 24, 2023)
3-14654457-A-G		not specified	Uncertain significance (Feb 05, 2024)
3-14654469-T-C		Severe hypotonia-psychomotor developmental delay-strabismus-cardiac septal defect syndrome • not specified	Uncertain significance (Jun 05, 2023)
3-14654495-T-G		not specified	Uncertain significance (Dec 21, 2023)
3-14654506-T-A		not specified	Likely benign (Oct 05, 2021)
3-14654515-A-G			Benign (Dec 31, 2019)
3-14654523-C-G		not specified	Uncertain significance (Sep 26, 2023)
3-14654525-A-G		not specified	Uncertain significance (Apr 22, 2024)
3-14655314-GA-G			Benign (May 13, 2021)
3-14655572-G-A		not specified	Uncertain significance (Jan 03, 2024)
3-14655599-T-A		not specified	Uncertain significance (Jan 26, 2023)
3-14655618-A-G			Likely benign (Apr 09, 2018)
3-14655639-T-C		CCDC174-related disorder	Likely benign (Aug 12, 2019)
3-14655811-A-G			Benign (May 10, 2021)
3-14658929-G-A		CCDC174-related disorder	Likely benign (Jun 29, 2018)
3-14658932-A-G		CCDC174-related disorder	Likely benign (Apr 06, 2022)
3-14661341-A-AT			Benign (May 27, 2021)
3-14661475-C-A		Severe hypotonia-psychomotor developmental delay-strabismus-cardiac septal defect syndrome	Benign (Jul 14, 2021)
3-14661547-A-G		not specified	Uncertain significance (Jul 25, 2023)
3-14661587-G-A		CCDC174-related disorder	Benign (Dec 31, 2019)
3-14661623-C-G		not specified	Uncertain significance (Mar 21, 2022)
3-14661645-C-T		not specified	Likely benign (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC174	protein_coding	protein_coding	ENST00000383794	11	20896

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.14e-8	0.974	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0441	259	261	0.992	0.0000145	3080
Missense in Polyphen		32	34.319	0.93244		374
Synonymous	-0.217	92	89.4	1.03	0.00000495	839
Loss of Function	2.13	16	28.2	0.568	0.00000160	327

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000307	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000564	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000243	0.000229
Middle Eastern	0.0000564	0.0000544
South Asian	0.000523	0.000490
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably involved in neuronal development. {ECO:0000269|PubMed:26358778}.

Recessive Scores

• pRec: 0.0979

Intolerance Scores

• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.65

Haploinsufficiency Scores

• pHI: 0.0587
• hipred: N
• hipred_score: 0.331
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc174
• 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

• Cellular component: nucleus;nucleoplasm
• Molecular function: protein binding