DNALI1

dynein axonemal light intermediate chain 1

Basic information

Region (hg38): 1:37556919-37566857

Links

ENSG00000163879 ∙ NCBI:7802 ∙ OMIM:602135 ∙ HGNC:14353 ∙ Uniprot:O14645 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 83 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 83	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	36792588

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DNALI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNALI1 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	3	4
missense			19	2	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	2
Total	0	0	20	3	5

Variants in DNALI1

This is a list of pathogenic ClinVar variants found in the DNALI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-37556952-C-T			Likely benign (May 24, 2018)
1-37556953-A-T		not specified	Uncertain significance (Mar 01, 2023)
1-37556966-G-T		not specified	Uncertain significance (Jan 29, 2024)
1-37556967-C-G		not specified	Likely benign (Dec 16, 2023)
1-37556980-A-G		not specified	Uncertain significance (Nov 21, 2022)
1-37557021-C-G			Benign (Dec 13, 2017)
1-37557606-C-T		not specified	Uncertain significance (May 16, 2024)
1-37557607-G-A		not specified	Uncertain significance (Jul 25, 2023)
1-37557670-C-G		not specified	Uncertain significance (Aug 08, 2023)
1-37557737-A-G		not specified	Uncertain significance (Dec 26, 2023)
1-37557745-C-T		not specified	Uncertain significance (Aug 01, 2022)
1-37559363-G-T		not specified	Uncertain significance (Jul 13, 2021)
1-37561590-C-T		not specified	Uncertain significance (May 03, 2023)
1-37561620-G-A		not specified	Uncertain significance (Jul 08, 2022)
1-37561637-A-T		not specified	Uncertain significance (Jul 12, 2023)
1-37561673-G-A		not specified	Uncertain significance (Apr 26, 2024)
1-37561682-G-A		not specified	Uncertain significance (Mar 27, 2023)
1-37561685-A-G		not specified	Uncertain significance (Jun 22, 2021)
1-37561692-A-G		not specified	Uncertain significance (Jan 30, 2024)
1-37561706-G-A		not specified	Uncertain significance (May 16, 2024)
1-37562090-T-C			Benign (Jun 20, 2018)
1-37562097-C-T		not specified	Uncertain significance (Nov 07, 2022)
1-37562129-G-A		not specified	Uncertain significance (Jan 30, 2024)
1-37562136-A-C			Likely benign (Apr 16, 2018)
1-37562162-C-T		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNALI1	protein_coding	protein_coding	ENST00000296218	6	9939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.12e-11	0.0527	125644	0	104	125748	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0154	168	169	0.997	0.00000983	1801
Missense in Polyphen		53	61.362	0.86373		654
Synonymous	-0.648	75	68.2	1.10	0.00000398	553
Loss of Function	0.00714	16	16.0	0.998	8.49e-7	173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000521	0.000518
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.000931	0.000924
European (Non-Finnish)	0.000476	0.000475
Middle Eastern	0.000273	0.000272
South Asian	0.000395	0.000392
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a dynamic role in flagellar motility.
• Pathway: Huntington,s disease - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.869
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.43

Haploinsufficiency Scores

• pHI: 0.172
• hipred: N
• hipred_score: 0.244
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dnali1

Gene ontology

• Biological process: inner dynein arm assembly
• Cellular component: cytoplasm;cilium;axoneme;filopodium;dynein complex;9+2 motile cilium
• Molecular function: motor activity;protein binding;dynein heavy chain binding