CCDC136

coiled-coil domain containing 136

Basic information

Region (hg38): 7:128790757-128822132

Links

ENSG00000128596 ∙ NCBI:64753 ∙ OMIM:611902 ∙ HGNC:22225 ∙ Uniprot:Q96JN2 ∙ 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 CCDC136 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC136 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				3	4	7
missense			61	6	3	70
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	61	9	7

Variants in CCDC136

This is a list of pathogenic ClinVar variants found in the CCDC136 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-128791523-A-C			Likely benign (Oct 01, 2022)
7-128794389-G-C		not specified	Uncertain significance (Nov 15, 2021)
7-128794446-A-G		not specified	Uncertain significance (Dec 21, 2022)
7-128794522-A-G		not specified	Uncertain significance (Sep 25, 2023)
7-128794558-G-A		not specified	Uncertain significance (Mar 25, 2024)
7-128801203-C-T		not specified	Uncertain significance (Apr 08, 2024)
7-128801243-A-C		not specified	Uncertain significance (Mar 20, 2023)
7-128801257-G-A		not specified	Uncertain significance (Sep 25, 2023)
7-128801299-C-T		not specified	Uncertain significance (Nov 12, 2021)
7-128801313-G-T		not specified	Uncertain significance (Jun 17, 2022)
7-128801359-G-T		not specified	Uncertain significance (Sep 27, 2021)
7-128801369-G-A		not specified	Uncertain significance (Jul 20, 2022)
7-128801393-T-G		not specified	Uncertain significance (Sep 20, 2023)
7-128801398-C-T		not specified	Uncertain significance (Mar 20, 2023)
7-128801428-G-A		not specified	Likely benign (Jul 08, 2022)
7-128801437-C-T		not specified	Uncertain significance (May 26, 2024)
7-128801473-G-A		not specified	Likely benign (May 09, 2023)
7-128801491-G-C			Benign (May 21, 2018)
7-128801502-G-C			Benign (May 21, 2018)
7-128804667-C-T		not specified	Uncertain significance (Feb 06, 2024)
7-128804724-A-G		not specified	Uncertain significance (Sep 22, 2021)
7-128804731-C-T		not specified	Uncertain significance (Aug 16, 2022)
7-128805436-T-C		not specified	Uncertain significance (Mar 31, 2023)
7-128805450-C-T		not specified	Uncertain significance (Feb 15, 2023)
7-128805767-G-A		not specified	Uncertain significance (Dec 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC136	protein_coding	protein_coding	ENST00000297788	17	31376

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.12e-14	1.00	124563	0	85	124648	0.000341

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	513	590	0.869	0.0000326	7624
Missense in Polyphen		188	223.07	0.84277		3042
Synonymous	1.17	212	235	0.903	0.0000129	1992
Loss of Function	3.28	31	58.0	0.535	0.00000263	751

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00122	0.00121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000714	0.000668
Finnish	0.00	0.00
European (Non-Finnish)	0.000313	0.000310
Middle Eastern	0.000714	0.000668
South Asian	0.0000327	0.0000327
Other	0.000516	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in acrosome formation in spermatogenesis and in fertilization. {ECO:0000250|UniProtKB:Q3TVA9}.

Recessive Scores

• pRec: 0.0998

Intolerance Scores

• rvis_EVS: 0.3
• rvis_percentile_EVS: 71.68

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.132
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.285

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc136
• Phenotype: cellular phenotype; reproductive system phenotype

Zebrafish Information Network

• Gene name: ccdc136b
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: acrosome assembly;spermatogenesis;single fertilization
• Cellular component: acrosomal membrane;integral component of membrane