ARMCX5

armadillo repeat containing X-linked 5, the group of Armadillo repeat containing

Basic information

Region (hg38): X:102599168-102604159

Links

ENSG00000125962 ∙ NCBI:64860 ∙ OMIM:301047 ∙ HGNC:25772 ∙ Uniprot:Q6P1M9 ∙ 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 ARMCX5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARMCX5 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				1		1
missense			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in ARMCX5

This is a list of pathogenic ClinVar variants found in the ARMCX5 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-102602146-T-C		not specified	Uncertain significance (Dec 21, 2022)
X-102602167-G-A		not specified	Uncertain significance (Aug 10, 2021)
X-102602250-G-C		not specified	Uncertain significance (May 13, 2024)
X-102602310-G-A		not specified	Uncertain significance (Mar 25, 2024)
X-102602314-C-T		not specified	Uncertain significance (May 28, 2024)
X-102602392-C-T		not specified	Uncertain significance (Dec 20, 2023)
X-102602427-C-T		not specified	Uncertain significance (Oct 12, 2021)
X-102602440-G-A		not specified	Uncertain significance (Jan 30, 2024)
X-102602460-A-G		not specified	Uncertain significance (Jan 17, 2024)
X-102602481-T-C		not specified	Uncertain significance (Oct 25, 2023)
X-102602506-C-G		not specified	Uncertain significance (Mar 25, 2024)
X-102602541-A-G		not specified	Uncertain significance (Mar 20, 2024)
X-102602545-G-T		not specified	Uncertain significance (Jul 27, 2022)
X-102602546-G-T		not specified	Uncertain significance (Jul 27, 2022)
X-102602626-C-T		not specified	Uncertain significance (May 08, 2024)
X-102602630-T-G		not specified	Uncertain significance (Mar 02, 2023)
X-102602651-A-G		not specified	Uncertain significance (Feb 17, 2024)
X-102602850-G-A		not specified	Uncertain significance (Dec 18, 2023)
X-102602851-G-C		not specified	Uncertain significance (Mar 26, 2024)
X-102602943-C-T		not specified	Uncertain significance (Oct 05, 2022)
X-102603123-C-G		not specified	Uncertain significance (Oct 25, 2023)
X-102603222-G-A		not specified	Uncertain significance (Feb 05, 2024)
X-102603275-C-G		ARMCX5-related disorder • not specified	Uncertain significance (Jan 26, 2022)
X-102603290-C-T			Likely benign (Dec 01, 2022)
X-102603297-C-A		not specified	Uncertain significance (Apr 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARMCX5	protein_coding	protein_coding	ENST00000604957	1	4992

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0334	0.931	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	156	197	0.792	0.0000133	3667
Missense in Polyphen		34	60.41	0.56282		1247
Synonymous	0.00132	72	72.0	1.00	0.00000499	1098
Loss of Function	1.82	4	10.3	0.389	7.03e-7	230

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

Intolerance Scores

• loftool: 0.156
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.0585
• hipred: N
• hipred_score: 0.132
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: Armcx5

Gene ontology

• Molecular function: protein binding