CARD6

caspase recruitment domain family member 6, the group of Caspase recruitment domain containing

Basic information

Region (hg38): 5:40841308-40860175

Links

ENSG00000132357 ∙ NCBI:84674 ∙ OMIM:609986 ∙ HGNC:16394 ∙ Uniprot:Q9BX69 ∙ 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 CARD6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CARD6 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						0
missense			50	9	4	63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	9	4

Variants in CARD6

This is a list of pathogenic ClinVar variants found in the CARD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-40841392-G-A		not specified	Uncertain significance (Sep 26, 2022)
5-40841477-C-T		not specified	Uncertain significance (May 20, 2024)
5-40841660-G-A			Benign (Apr 13, 2018)
5-40843178-C-T		not specified	Uncertain significance (Dec 05, 2022)
5-40843192-G-C		not specified	Uncertain significance (Dec 28, 2023)
5-40843196-G-A		not specified	Conflicting classifications of pathogenicity (Dec 01, 2023)
5-40843343-G-A		not specified	Uncertain significance (Sep 16, 2021)
5-40843347-T-G		not specified	Likely benign (Aug 11, 2022)
5-40843418-G-C		not specified	Uncertain significance (Oct 29, 2024)
5-40843422-G-A			Benign (Apr 13, 2018)
5-40843448-A-G			Benign (Jul 24, 2018)
5-40843456-T-G		not specified	Uncertain significance (Jul 05, 2024)
5-40843457-G-A		not specified	Uncertain significance (Mar 01, 2023)
5-40843583-G-A		not specified	Likely benign (Dec 18, 2023)
5-40843584-T-C		not specified	Uncertain significance (Aug 05, 2024)
5-40843596-G-A		not specified	Uncertain significance (Mar 20, 2024)
5-40843656-A-C		not specified	Uncertain significance (Dec 08, 2023)
5-40843659-G-A			Benign (Apr 13, 2018)
5-40843683-A-T		not specified	Uncertain significance (Oct 28, 2024)
5-40852222-G-A		not specified	Uncertain significance (Jun 24, 2022)
5-40852275-T-C		not specified	Uncertain significance (Oct 27, 2022)
5-40852302-G-A		not specified	Uncertain significance (Apr 05, 2023)
5-40852350-G-A		not specified	Uncertain significance (Jan 31, 2024)
5-40852362-A-G		not specified	Likely benign (Dec 21, 2022)
5-40852373-C-G		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CARD6	protein_coding	protein_coding	ENST00000254691	3	18990

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.39e-13	0.0817	120864	64	4819	125747	0.0196

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.414	541	515	1.05	0.0000249	6792
Missense in Polyphen		74	71.037	1.0417		1044
Synonymous	1.25	168	190	0.884	0.00000923	2019
Loss of Function	0.580	21	24.1	0.872	0.00000125	337

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0147	0.0146
Ashkenazi Jewish	0.0292	0.0291
East Asian	0.000544	0.000544
Finnish	0.0332	0.0333
European (Non-Finnish)	0.0278	0.0277
Middle Eastern	0.000544	0.000544
South Asian	0.00719	0.00715
Other	0.0222	0.0224

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in apoptosis.
• Pathway: NOD-like receptor signaling pathway - Homo sapiens (human);Nucleotide-binding Oligomerization Domain (NOD) pathway (Consensus)

Recessive Scores

• pRec: 0.0685

Intolerance Scores

• rvis_EVS: 1.79
• rvis_percentile_EVS: 96.87

Haploinsufficiency Scores

• pHI: 0.0353
• hipred: N
• hipred_score: 0.318
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.394

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Card6

Gene ontology

• Biological process: apoptotic process;regulation of apoptotic process
• Molecular function: protein binding