CHML

CHM like Rab escort protein

Basic information

Region (hg38): 1:241628850-241640369

Links

ENSG00000203668 ∙ NCBI:1122 ∙ OMIM:118825 ∙ HGNC:1941 ∙ Uniprot:P26374 ∙ 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 CHML gene.

• Inborn genetic diseases (34 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHML 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			22	3		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			9	1	1	11
Total	0	0	31	4	1

Variants in CHML

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

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

Position	Type	Phenotype	Significance	ClinVar
1-241633926-T-C		not specified	Uncertain significance (Jan 26, 2023)
1-241633993-G-T		not specified	Uncertain significance (Feb 26, 2024)
1-241634088-G-A		not specified	Uncertain significance (Jan 26, 2023)
1-241634172-G-A		not specified	Uncertain significance (May 09, 2022)
1-241634259-T-G		not specified	Uncertain significance (Dec 04, 2023)
1-241634268-G-C		not specified	Uncertain significance (Aug 30, 2021)
1-241634283-C-G		not specified	Uncertain significance (Feb 27, 2023)
1-241634295-A-T		not specified	Uncertain significance (Sep 22, 2023)
1-241634298-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-241634326-G-C		not specified	Uncertain significance (Jun 01, 2023)
1-241634333-T-C		not specified	Uncertain significance (Mar 07, 2024)
1-241634359-A-T		not specified	Uncertain significance (Mar 07, 2023)
1-241634383-C-G		not specified	Uncertain significance (Aug 13, 2021)
1-241634533-C-T		not specified	Uncertain significance (Jan 12, 2024)
1-241634604-C-A		not specified	Uncertain significance (May 24, 2023)
1-241634680-A-C		not specified	Uncertain significance (Jun 30, 2022)
1-241634710-T-C		not specified	Uncertain significance (Jan 02, 2024)
1-241634715-C-T		not specified	Uncertain significance (Dec 03, 2021)
1-241634752-C-T		not specified	Likely benign (May 25, 2022)
1-241634757-T-C		not specified	Uncertain significance (Dec 20, 2023)
1-241634868-A-C		not specified	Uncertain significance (Apr 17, 2023)
1-241634979-G-A		not specified	Uncertain significance (Dec 20, 2021)
1-241635130-T-C		not specified	Uncertain significance (Jun 13, 2023)
1-241635177-T-A		not specified	Uncertain significance (May 13, 2022)
1-241635234-T-G		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHML	protein_coding	protein_coding	ENST00000366553	1	7078

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000400	0.959	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0429	342	340	1.01	0.0000168	4325
Missense in Polyphen		86	107.14	0.80266		1390
Synonymous	-0.950	141	127	1.11	0.00000683	1253
Loss of Function	1.86	10	18.7	0.535	8.89e-7	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
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

• Function: FUNCTION: Substrate-binding subunit (component A) of the Rab geranylgeranyltransferase (GGTase) complex. Binds unprenylated Rab proteins and presents the substrate peptide to the catalytic component B. The component A is thought to be regenerated by transferring its prenylated Rab back to the donor membrane. Less effective than CHM in supporting prenylation of Rab3 family. {ECO:0000269|PubMed:12356470, ECO:0000269|PubMed:15186776, ECO:0000269|PubMed:8294464}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation (Consensus)

Intolerance Scores

• loftool: 0.220
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.11

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.180
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.357

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chml

Gene ontology

• Biological process: intracellular protein transport;small GTPase mediated signal transduction;protein geranylgeranylation;positive regulation of GTPase activity;post-translational protein modification
• Cellular component: nucleus;nucleoplasm;cytosol;Rab-protein geranylgeranyltransferase complex
• Molecular function: GDP-dissociation inhibitor activity;GTPase activator activity;Rab GTPase binding