DMXL1

Dmx like 1, the group of WD repeat domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 5:119037772-119249138

Links

ENSG00000172869 ∙ NCBI:1657 ∙ OMIM:605671 ∙ HGNC:2937 ∙ Uniprot:Q9Y485 ∙ 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 DMXL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DMXL1 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				19	25	44
missense			156	13	25	194
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				4	2	6
non coding					2	2
Total	0	0	156	32	53

Variants in DMXL1

This is a list of pathogenic ClinVar variants found in the DMXL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-119071605-C-T		DMXL1-related disorder	Benign (Jul 23, 2018)
5-119071646-A-G		not specified	Uncertain significance (Dec 05, 2022)
5-119101985-A-C		DMXL1-related disorder	Likely benign (Aug 09, 2019)
5-119105212-A-T		not specified	Uncertain significance (May 31, 2023)
5-119105229-T-C		not specified	Uncertain significance (Mar 18, 2024)
5-119105235-A-G		not specified	Uncertain significance (Oct 17, 2023)
5-119105242-A-G		not specified	Uncertain significance (Jun 27, 2022)
5-119105253-C-T		not specified	Uncertain significance (Dec 02, 2022)
5-119110178-A-G		not specified	Likely benign (May 03, 2023)
5-119116178-T-G		DMXL1-related disorder	Benign (Feb 28, 2019)
5-119116201-G-A		DMXL1-related disorder	Benign (Jul 10, 2019)
5-119116231-C-T		not specified	Uncertain significance (Apr 27, 2023)
5-119116244-C-T		DMXL1-related disorder	Benign (Dec 31, 2019)
5-119116248-G-A		not specified	Uncertain significance (Oct 20, 2023)
5-119116256-T-G		DMXL1-related disorder	Likely benign (Nov 18, 2019)
5-119118925-A-G		not specified	Uncertain significance (Jan 11, 2023)
5-119118957-T-C		not specified	Uncertain significance (Aug 08, 2023)
5-119118973-C-G		not specified	Uncertain significance (May 28, 2024)
5-119118985-G-A		not specified	Uncertain significance (Jun 12, 2023)
5-119118992-A-G		DMXL1-related disorder	Likely benign (Mar 20, 2019)
5-119120976-T-C		DMXL1-related disorder	Benign (Jun 12, 2019)
5-119121007-T-A		not specified	Uncertain significance (Feb 06, 2024)
5-119121010-C-G		not specified	Uncertain significance (Jun 24, 2022)
5-119121014-C-G		not specified	Uncertain significance (Dec 19, 2023)
5-119121026-A-G		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DMXL1	protein_coding	protein_coding	ENST00000311085	43	211367

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.81e-9	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.489	1595	1.54e+3	1.03	0.0000773	19862
Missense in Polyphen		457	593.32	0.77024		7578
Synonymous	-2.73	620	539	1.15	0.0000267	5783
Loss of Function	9.39	19	138	0.138	0.00000696	1785

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000375	0.000362
Ashkenazi Jewish	0.000796	0.000794
East Asian	0.000109	0.000109
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000327	0.000325
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.501
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.89

Haploinsufficiency Scores

• pHI: 0.713
• hipred: Y
• hipred_score: 0.591
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.422

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dmxl1

Gene ontology

• Biological process: vacuolar acidification
• Cellular component: RAVE complex