ARMCX1

armadillo repeat containing X-linked 1, the group of Armadillo repeat containing

Basic information

Region (hg38): X:101550547-101554700

Links

ENSG00000126947 ∙ NCBI:51309 ∙ OMIM:300362 ∙ HGNC:18073 ∙ Uniprot:Q9P291 ∙ 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 ARMCX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARMCX1 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				2	1	3
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	1

Variants in ARMCX1

This is a list of pathogenic ClinVar variants found in the ARMCX1 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-101552945-G-A			Benign (May 17, 2018)
X-101553026-C-A		not specified	Uncertain significance (Sep 28, 2022)
X-101553028-A-G		not specified	Uncertain significance (Oct 06, 2023)
X-101553032-C-T			Likely benign (Mar 01, 2023)
X-101553036-A-G		not specified	Uncertain significance (Sep 26, 2022)
X-101553061-C-T		not specified	Uncertain significance (Jan 26, 2023)
X-101553120-G-A		not specified	Uncertain significance (Mar 04, 2024)
X-101553175-T-C		not specified	Uncertain significance (Dec 15, 2023)
X-101553310-C-T		not specified	Uncertain significance (Jul 13, 2022)
X-101553423-G-A		not specified	Uncertain significance (Aug 02, 2023)
X-101553436-C-A		not specified	Uncertain significance (Dec 13, 2021)
X-101553520-A-C		not specified	Uncertain significance (Mar 01, 2024)
X-101553754-G-C		not specified	Uncertain significance (Aug 08, 2023)
X-101553825-C-T		not specified	Uncertain significance (Feb 21, 2024)
X-101553898-A-G		not specified	Uncertain significance (Jun 13, 2024)
X-101553900-T-A		not specified	Uncertain significance (Sep 27, 2022)
X-101554229-A-G			Likely benign (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARMCX1	protein_coding	protein_coding	ENST00000372829	1	4170

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0727	0.878	125736	1	2	125739	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	107	175	0.612	0.0000133	2963
Missense in Polyphen		50	86.298	0.57939		1577
Synonymous	0.463	67	72.0	0.931	0.00000596	929
Loss of Function	1.66	3	8.12	0.370	6.56e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000776	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000129	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000536	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates mitochondrial transport during axon regeneration. Increases the proportion of motile mitochondria by recruiting stationary mitochondria into the motile pool. Enhances mitochondria movement and neurite growth in both adult axons and embryonic neurons. Promotes neuronal survival and axon regeneration after nerve injury. May link mitochondria to the Trak1-kinesin motor complex via its interaction with MIRO1. {ECO:0000250|UniProtKB:Q9CX83}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.115
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.0874
• hipred: N
• hipred_score: 0.425
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Armcx1

Gene ontology

• Cellular component: mitochondrial outer membrane;integral component of membrane
• Molecular function: protein binding