AXDND1

protein-coding

axonemal dynein light chain domain containing 1

Gene summary

Predicted to be involved in manchette assembly. Predicted to act upstream of or within several processes, including axoneme assembly; male gonad development; and spermatogonial cell division. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C1orf125

MANE transcript

NM_144696.6

Inheritance

—

ClinVar variants

P:1U:137B:11

Top phenotype

Nephrotic syndrome, type 2

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr1:179,365,720-179,554,735

External References & Databases

Ensembl (ENSG00000162779)

Transcript & Mutation Effects

hg38 • Region Span ~189.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AXDND1 variants in ClinVar

15 Conditions Cataloged

not specifiedTotal: 151

not providedTotal: 124

Nephrotic syndrome, type 2Total: 81

Steroid-resistant nephrotic syndromeTotal: 36

NPHS2-related disorderTotal: 11

Inborn genetic diseasesTotal: 8

Nephrotic syndromeTotal: 6

Male infertilityTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144696.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			134 clinvar	11 clinvar		145
nonsense		1 clinvar				1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	137	11	0	149

Highest pathogenic variant AF is 0.000236677

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144696.6	RefSeq	NP_653297.3	25	MANE Select
ENST00000367618.8	Ensembl	ENSP00000356590.3	25	MANE Select
ENST00000434088.1	Ensembl	ENSP00000391716.1	22	Standard
ENST00000508229.5	Ensembl	ENSP00000422992.1	2	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367618
Coding exons: 25
Length: 189016
Individuals with no LoFs: 125391
Homozygous LoFs: 0
Heterozygous LoFs: 357
Defined: 125748
p: 0.00142

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.298	516	497	1.04	0.0000236	6695
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0012	0.0012	notable
Latino/Admixed American	0.0012	0.0012	notable
Ashkenazi Jewish	0.0020	0.0020	notable
East Asian	0.00072	0.00071	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.0014	0.0014	notable
South Asian	0.0032	0.0031	notable
Other	0.0011	0.00098	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0838

Intolerance Scores

RVIS EVS: 0.61
RVIS percentile EVS: 82.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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