C2CD6

C2 calcium dependent domain containing 6, the group of C2 domain containing

Basic information

Region (hg38): 2:201487420-201619178

Previous symbols: [ "ALS2CR11" ]

Links

ENSG00000155754 ∙ NCBI:151254 ∙ OMIM:619776 ∙ HGNC:14438 ∙ Uniprot:Q53TS8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 68	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	31985809

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C2CD6 gene.

• Inborn genetic diseases (23 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C2CD6 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				2		2
missense			22	3	1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	5	1

Variants in C2CD6

This is a list of pathogenic ClinVar variants found in the C2CD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-201487665-A-G		not specified	Likely benign (Jan 05, 2022)
2-201487719-A-T		not specified	Uncertain significance (Dec 03, 2021)
2-201487740-G-A		Spermatogenic failure 68	Uncertain significance (Apr 04, 2024)
2-201487797-G-A		not specified	Uncertain significance (Mar 23, 2022)
2-201487820-A-G		Malignant tumor of prostate	Uncertain significance (-)
2-201487868-A-T		not specified	Uncertain significance (May 16, 2022)
2-201491189-T-C		not specified	Uncertain significance (Nov 10, 2021)
2-201491200-A-G		not specified	Uncertain significance (Aug 01, 2022)
2-201491224-A-T		not specified	Uncertain significance (Jun 07, 2023)
2-201491228-G-T		not specified	Uncertain significance (Jun 07, 2023)
2-201491297-C-T		not specified	Uncertain significance (Aug 30, 2021)
2-201491305-T-C		not specified	Uncertain significance (May 30, 2023)
2-201491514-C-A		not specified	Uncertain significance (Dec 17, 2023)
2-201491719-T-G		not specified	Uncertain significance (Jun 03, 2022)
2-201491843-G-C		not specified	Uncertain significance (Mar 14, 2023)
2-201491897-G-A		not specified	Uncertain significance (Nov 08, 2022)
2-201491905-C-T		not specified	Likely benign (Sep 20, 2023)
2-201492074-A-C		not specified	Uncertain significance (Jul 17, 2023)
2-201492227-C-T		not specified	Uncertain significance (Jan 23, 2023)
2-201492251-T-C		not specified	Uncertain significance (Nov 30, 2022)
2-201492262-G-A		not specified	Uncertain significance (Nov 21, 2023)
2-201492266-T-C		not specified	Uncertain significance (Apr 25, 2022)
2-201492326-T-C		not specified	Uncertain significance (Aug 03, 2022)
2-201492362-T-C		not specified	Likely benign (Feb 13, 2024)
2-201492363-C-G			Benign (Apr 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C2CD6	protein_coding	protein_coding	ENST00000439140	16	131754

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.98e-16	1.00	125721	0	21	125742	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.82	620	851	0.728	0.0000413	12024
Missense in Polyphen		123	166.42	0.73909		2445
Synonymous	3.27	235	308	0.763	0.0000156	3277
Loss of Function	3.31	36	64.7	0.556	0.00000307	1043

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000302	0.0000302
Ashkenazi Jewish	0.000204	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000113	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.000177	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 2.54
• rvis_percentile_EVS: 98.71

Haploinsufficiency Scores

• pHI: 0.223
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: C2cd6b

Gene ontology

• Molecular function: protein binding