AXDND1

axonemal dynein light chain domain containing 1

Basic information

Region (hg38): 1:179365719-179554735

Previous symbols: [ "C1orf125" ]

Links

ENSG00000162779 ∙ NCBI:126859 ∙ ∙ HGNC:26564 ∙ Uniprot:Q5T1B0 ∙ 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 AXDND1 gene.

• not provided (112 variants)
• Nephrotic syndrome, type 2 (62 variants)
• Inborn genetic diseases (42 variants)
• Steroid-resistant nephrotic syndrome (13 variants)
• not specified (8 variants)
• Idiopathic nephrotic syndrome (4 variants)
• Focal segmental glomerulosclerosis (3 variants)
• Nephrotic syndrome (3 variants)
• NPHS2-related condition (2 variants)
• Nephrotic syndrome, type 2, susceptibility to (1 variants)
• Chronic kidney disease (1 variants)
• Kidney disorder (1 variants)
• Nephrotic range proteinuria (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AXDND1 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			34	6		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	3	26	28	61	17	135
Total	3	26	62	67	17

Highest pathogenic variant AF is 0.0000131

Variants in AXDND1

This is a list of pathogenic ClinVar variants found in the AXDND1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-179366547-C-G		not specified	Uncertain significance (Nov 22, 2021)
1-179366552-T-A		not specified	Uncertain significance (Jan 16, 2024)
1-179368829-A-C		not specified	Uncertain significance (May 04, 2023)
1-179368829-A-G		not specified	Uncertain significance (Aug 13, 2021)
1-179368913-G-A		not specified	Uncertain significance (Nov 01, 2022)
1-179368917-A-G		not specified	Uncertain significance (Apr 25, 2023)
1-179368967-C-T		not specified	Uncertain significance (Jun 12, 2023)
1-179378710-T-G		not specified	Uncertain significance (Jan 25, 2023)
1-179378717-G-A		not specified	Likely benign (May 05, 2023)
1-179379463-G-T		not specified	Uncertain significance (Dec 01, 2022)
1-179383457-A-C		not specified	Uncertain significance (May 18, 2023)
1-179383491-A-G		not specified	Uncertain significance (Feb 03, 2022)
1-179383513-T-A		not specified	Uncertain significance (Oct 21, 2021)
1-179383540-C-G		not specified	Uncertain significance (Mar 22, 2022)
1-179385257-T-C		not specified	Uncertain significance (Oct 20, 2023)
1-179393976-C-T		Non-obstructive azoospermia	Likely pathogenic (May 08, 2024)
1-179394010-A-G		not specified	Uncertain significance (Feb 06, 2024)
1-179395115-G-A		not specified	Uncertain significance (Aug 08, 2022)
1-179395121-A-G		not specified	Uncertain significance (Dec 12, 2023)
1-179411149-A-G		not specified	Likely benign (Dec 18, 2023)
1-179411153-G-A		not specified	Uncertain significance (Jun 01, 2023)
1-179411162-C-A		not specified	Uncertain significance (Jun 06, 2023)
1-179411171-T-C		not specified	Uncertain significance (Dec 20, 2023)
1-179411184-G-T		not specified	Uncertain significance (Mar 05, 2024)
1-179411247-C-T		not specified	Uncertain significance (Jul 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AXDND1	protein_coding	protein_coding	ENST00000367618	25	189016

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.31e-26	0.0528	125391	0	357	125748	0.00142

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.298	516	497	1.04	0.0000236	6695
Missense in Polyphen		58	58.867	0.98528		752
Synonymous	0.145	176	178	0.986	0.00000880	1754
Loss of Function	1.61	47	60.5	0.777	0.00000318	777

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00237	0.00236
Ashkenazi Jewish	0.00204	0.00199
East Asian	0.000724	0.000707
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00143	0.00142
Middle Eastern	0.000724	0.000707
South Asian	0.00317	0.00311
Other	0.00105	0.000978

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0838

Intolerance Scores

• rvis_EVS: 0.61
• rvis_percentile_EVS: 82.93

Haploinsufficiency Scores

• pHI: 0.0763
• hipred: N
• hipred_score: 0.145

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: Axdnd1