ARMCX2

armadillo repeat containing X-linked 2, the group of Armadillo repeat containing

Basic information

Region (hg38): X:101655281-101659850

Links

ENSG00000184867 ∙ NCBI:9823 ∙ OMIM:300363 ∙ HGNC:16869 ∙ Uniprot:Q7L311 ∙ 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 ARMCX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARMCX2 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				3		3
missense			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	3	0

Variants in ARMCX2

This is a list of pathogenic ClinVar variants found in the ARMCX2 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-101655850-T-C		not specified	Uncertain significance (Jun 10, 2022)
X-101655900-T-C			Likely benign (Nov 01, 2022)
X-101656299-G-T			Likely benign (May 01, 2022)
X-101656529-A-G		not specified	Uncertain significance (May 24, 2023)
X-101656655-G-A		not specified	Uncertain significance (Aug 10, 2021)
X-101656706-C-T		not specified	Uncertain significance (Nov 27, 2023)
X-101656765-G-A		not specified	Uncertain significance (Feb 28, 2024)
X-101656910-T-C		not specified	Uncertain significance (Mar 04, 2024)
X-101656915-G-A		not specified	Uncertain significance (Aug 27, 2024)
X-101656961-C-G		not specified	Uncertain significance (Jul 13, 2021)
X-101656961-C-T		not specified	Uncertain significance (Mar 20, 2023)
X-101656969-T-G		not specified	Uncertain significance (Aug 27, 2024)
X-101656996-C-T		not specified	Uncertain significance (Nov 18, 2024)
X-101657080-G-C		not specified	Uncertain significance (Mar 18, 2024)
X-101657084-C-T		not specified	Uncertain significance (Nov 23, 2024)
X-101657131-T-C		not specified	Uncertain significance (Aug 21, 2023)
X-101657159-C-T		not specified	Uncertain significance (Jun 01, 2023)
X-101657192-C-T		not specified	Uncertain significance (Mar 23, 2022)
X-101657225-C-A		not specified	Uncertain significance (Oct 31, 2023)
X-101657246-C-A		not specified	Uncertain significance (Jun 07, 2023)
X-101657276-C-G		not specified	Uncertain significance (Sep 26, 2024)
X-101657276-C-T		not specified	Uncertain significance (Nov 03, 2022)
X-101657295-C-A			Likely benign (Apr 01, 2023)
X-101657314-G-C		not specified	Uncertain significance (May 31, 2023)
X-101657368-G-T		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARMCX2	protein_coding	protein_coding	ENST00000328766	1	4610

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.692	0.304	125728	3	1	125732	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	192	261	0.736	0.0000206	4065
Missense in Polyphen		45	99.671	0.45148		1750
Synonymous	-0.775	115	105	1.10	0.00000885	1403
Loss of Function	2.32	1	8.16	0.123	5.11e-7	192

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000144	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000124	0.00000879
Middle Eastern	0.000144	0.000109
South Asian	0.0000524	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate the dynamics and distribution of mitochondria in neural cells. {ECO:0000250|UniProtKB:Q6A058}.

Recessive Scores

• pRec: 0.0983

Intolerance Scores

• loftool: 0.102
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.203
• hipred: N
• hipred_score: 0.274
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.503

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Armcx2

Gene ontology

• Cellular component: mitochondrial outer membrane;integral component of membrane