NANOS1

nanos C2HC-type zinc finger 1, the group of Zinc fingers C2HC-type

Basic information

Region (hg38): 10:119029713-119033730

Links

ENSG00000188613 ∙ NCBI:340719 ∙ OMIM:608226 ∙ HGNC:23044 ∙ Uniprot:Q8WY41 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Supportive), mode of inheritance: AD
• spermatogenic failure 12 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 12	AD	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	23315541

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NANOS1 gene.

• Inborn genetic diseases (31 variants)
• not provided (10 variants)
• - (2 variants)
• Spermatogenic failure 12 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NANOS1 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	2
missense			29	3	2	34
nonsense						0
start loss						0
frameshift						0
inframe indel			1	1	2	4
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	30	5	6

Variants in NANOS1

This is a list of pathogenic ClinVar variants found in the NANOS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-119029751-G-C			Benign (Nov 12, 2018)
10-119029820-G-T		not specified	Uncertain significance (Feb 11, 2022)
10-119029839-G-A		not specified	Uncertain significance (Sep 27, 2022)
10-119029842-G-A		not specified	Uncertain significance (Oct 26, 2022)
10-119029853-C-G		not specified	Uncertain significance (Apr 25, 2023)
10-119029854-C-T		not specified	Uncertain significance (Nov 09, 2021)
10-119029896-C-A		not specified	Uncertain significance (Apr 07, 2023)
10-119029896-C-T		not specified	Uncertain significance (Feb 26, 2024)
10-119029901-C-A			Benign (Jul 15, 2020)
10-119029991-G-A		not specified	Uncertain significance (May 26, 2022)
10-119030010-A-G		not specified	Uncertain significance (Apr 07, 2023)
10-119030025-C-T		not specified	Uncertain significance (Jan 20, 2023)
10-119030030-CCCT-C		Spermatogenic failure 12 • NANOS1-related disorder	Benign/Likely benign (Dec 14, 2023)
10-119030036-T-A			Benign (Jun 09, 2021)
10-119030043-C-T		not specified	Uncertain significance (Dec 19, 2022)
10-119030063-C-A		not specified	Uncertain significance (Dec 01, 2022)
10-119030064-A-C		not specified	Uncertain significance (Sep 14, 2021)
10-119030066-A-G		not specified	Likely benign (Apr 07, 2023)
10-119030075-G-A		not specified	Uncertain significance (Sep 22, 2023)
10-119030082-G-C		not specified	Uncertain significance (Mar 07, 2023)
10-119030082-GGGCGCTGGGGCC-G		NANOS1-related disorder	Likely benign (Feb 01, 2023)
10-119030154-C-A		not specified	Uncertain significance (Aug 08, 2022)
10-119030174-A-G		not specified	Likely benign (Apr 07, 2023)
10-119030177-G-A		not specified	Uncertain significance (Apr 07, 2023)
10-119030211-G-A		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NANOS1	protein_coding	protein_coding	ENST00000425699	1	4627

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.541	0.407	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	52	82.6	0.629	0.00000393	1773
Missense in Polyphen		9	18.706	0.48112		260
Synonymous	-0.666	46	40.6	1.13	0.00000210	684
Loss of Function	1.41	0	2.31	0.00	9.90e-8	55

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

• Function: FUNCTION: May act as a translational repressor which regulates translation of specific mRNAs by forming a complex with PUM2 that associates with the 3'-UTR of mRNA targets. Capable of interfering with the proadhesive and anti-invasive functions of E-cadherin. Up-regulates the production of MMP14 to promote tumor cell invasion. {ECO:0000269|PubMed:17047063, ECO:0000269|PubMed:18223680}.
• Disease: DISEASE: Spermatogenic failure 12 (SPGF12) [MIM:615413]: An infertility disorder caused by spermatogenesis defects. It results in decreased sperm motility, concentration, and multiple sperm structural defects. Non-obstructive azoospermia, oligozoospermia and oligo-astheno-teratozoospermia are features observed in SPGF12 patients. {ECO:0000269|PubMed:23315541}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.612

Haploinsufficiency Scores

• pHI: 0.201
• hipred: N
• hipred_score: 0.238
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.766

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nanos1
• Phenotype: normal phenotype

Gene ontology

• Biological process: regulation of cell growth;tissue homeostasis;posttranscriptional regulation of gene expression;epithelial cell migration;cell migration;negative regulation of translation;cerebellar neuron development;positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
• Cellular component: cytoplasm;perinuclear region of cytoplasm
• Molecular function: RNA binding;protein binding;zinc ion binding;translation repressor activity