CMC4

C-X9-C motif containing 4

Basic information

Region (hg38): X:155061622-155071136

Previous symbols: [ "MTCP1", "MTCP1NB" ]

Links

ENSG00000182712 ∙ NCBI:100272147 ∙ OMIM:301088 ∙ HGNC:35428 ∙ Uniprot:P56277 ∙ 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 CMC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMC4 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	8	0	0

Variants in CMC4

This is a list of pathogenic ClinVar variants found in the CMC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-155061857-A-G		not specified	Uncertain significance (Jun 27, 2022)
X-155061862-C-T		not specified	Uncertain significance (Dec 22, 2023)
X-155061901-C-G			Likely benign (-)
X-155061944-G-A		not specified	Uncertain significance (Dec 07, 2021)
X-155061979-A-G		not specified	Uncertain significance (Apr 07, 2022)
X-155063978-T-G		not specified	Uncertain significance (Nov 04, 2021)
X-155063983-A-G		not specified	Uncertain significance (Jun 22, 2021)
X-155064016-T-C		not specified	Uncertain significance (May 27, 2022)
X-155065650-G-C		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMC4	protein_coding	protein_coding	ENST00000369484	2	9741

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.158	0.650	124758	1	2	124761	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.170	24	26.5	0.907	0.00000221	433
Missense in Polyphen		7	8.2747	0.84595		146
Synonymous	-0.763	13	9.94	1.31	8.43e-7	114
Loss of Function	0.740	1	2.18	0.459	1.37e-7	44

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000234	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=Overexpressed in T-cell leukemia bearing a t(X;14) translocation. {ECO:0000269|PubMed:8361760}.
• Pathway: Metabolism of proteins;Mitochondrial protein import (Consensus)

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 63.81

Haploinsufficiency Scores

• pHI: 0.212
• hipred: N
• hipred_score: 0.150

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cmc4

Gene ontology

• Biological process: cell population proliferation
• Cellular component: mitochondrion;mitochondrial intermembrane space