MCCD1

mitochondrial coiled-coil domain 1

Basic information

Region (hg38): 6:31528962-31530232

Links

ENSG00000204511 ∙ NCBI:401250 ∙ OMIM:609624 ∙ HGNC:20668 ∙ Uniprot:P59942 ∙ 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 MCCD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCCD1 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			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in MCCD1

This is a list of pathogenic ClinVar variants found in the MCCD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31529087-C-A		not specified	Uncertain significance (Dec 13, 2022)
6-31529121-C-G		not specified	Uncertain significance (Nov 17, 2023)
6-31529135-G-A		not specified	Uncertain significance (Nov 14, 2024)
6-31529774-C-A		not specified	Uncertain significance (Oct 06, 2021)
6-31529781-G-A		not specified	Likely benign (Dec 22, 2023)
6-31529795-T-G		not specified	Uncertain significance (Sep 29, 2023)
6-31529840-G-A		not specified	Uncertain significance (Jun 29, 2023)
6-31529904-G-T		not specified	Uncertain significance (Sep 20, 2023)
6-31529928-G-T		not specified	Uncertain significance (Jun 05, 2024)
6-31529931-C-G		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MCCD1	protein_coding	protein_coding	ENST00000376191	2	1516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00193	0.510	123144	0	9	123153	0.0000365

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.388	64	55.8	1.15	0.00000279	738
Missense in Polyphen		12	10.873	1.1037		178
Synonymous	0.795	18	22.8	0.788	0.00000109	237
Loss of Function	0.126	4	4.28	0.934	2.53e-7	43

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000691	0.0000691
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000506	0.0000452
Middle Eastern	0.00	0.00
South Asian	0.0000660	0.0000659
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.791
• rvis_EVS: 0.88
• rvis_percentile_EVS: 88.96

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.135

Gene Damage Prediction

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

Gene ontology

• Cellular component: mitochondrion