CCDC74A

coiled-coil domain containing 74A

Basic information

Region (hg38): 2:131527675-131533666

Links

ENSG00000163040 ∙ NCBI:90557 ∙ ∙ HGNC:25197 ∙ Uniprot:Q96AQ1 ∙ 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 CCDC74A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC74A 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			52	3		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	4	0

Variants in CCDC74A

This is a list of pathogenic ClinVar variants found in the CCDC74A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-131527984-G-A		not specified	Uncertain significance (Dec 18, 2023)
2-131527995-G-A		not specified	Uncertain significance (Apr 07, 2023)
2-131527999-C-T		not specified	Uncertain significance (Apr 04, 2023)
2-131528004-C-T		not specified	Uncertain significance (May 30, 2023)
2-131528005-C-G		not specified	Uncertain significance (Apr 14, 2022)
2-131528020-C-T		not specified	Uncertain significance (Oct 27, 2021)
2-131528026-G-A		not specified	Uncertain significance (Aug 10, 2024)
2-131528041-G-A		not specified	Uncertain significance (Jun 16, 2024)
2-131528046-C-T		not specified	Uncertain significance (Dec 19, 2023)
2-131528050-C-G		not specified	Uncertain significance (Jun 22, 2024)
2-131528053-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-131528059-G-C		not specified	Uncertain significance (Feb 15, 2023)
2-131528102-C-G		not specified	Uncertain significance (Jul 29, 2023)
2-131528147-C-G		not specified	Uncertain significance (May 10, 2022)
2-131528159-G-C		not specified	Uncertain significance (Jan 27, 2025)
2-131528195-C-G		not specified	Uncertain significance (Feb 03, 2022)
2-131528203-T-G		not specified	Uncertain significance (Aug 04, 2023)
2-131528211-G-A		not specified	Uncertain significance (May 10, 2022)
2-131529653-A-G		not specified	Uncertain significance (Mar 16, 2022)
2-131530600-T-C		not specified	Uncertain significance (Mar 16, 2022)
2-131530623-G-A		not specified	Uncertain significance (Dec 13, 2023)
2-131530638-T-A		not specified	Uncertain significance (Jan 04, 2025)
2-131530647-G-A		not specified	Uncertain significance (Jan 07, 2025)
2-131530656-G-C		not specified	Uncertain significance (Feb 28, 2024)
2-131530663-C-T		not specified	Uncertain significance (Aug 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC74A	protein_coding	protein_coding	ENST00000295171	8	5992

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.72e-19	0.000214	125643	1	102	125746	0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.220	226	217	1.04	0.0000121	2398
Missense in Polyphen		78	62.944	1.2392		818
Synonymous	-0.770	100	90.7	1.10	0.00000521	762
Loss of Function	-1.53	24	17.1	1.40	8.14e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000821	0.000818
Ashkenazi Jewish	0.000118	0.0000992
East Asian	0.00267	0.00267
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000258	0.000255
Middle Eastern	0.00267	0.00267
South Asian	0.000237	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.933
• rvis_EVS: 1.84
• rvis_percentile_EVS: 97.1

Haploinsufficiency Scores

• pHI: 0.0841
• hipred: N
• hipred_score: 0.187
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.192

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc74a