NASP

nuclear autoantigenic sperm protein, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 1:45583846-45618904

Links

ENSG00000132780 ∙ NCBI:4678 ∙ OMIM:603185 ∙ HGNC:7644 ∙ Uniprot:P49321 ∙ 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 NASP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NASP 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			53	9		62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	10	1

Variants in NASP

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

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

Position	Type	Phenotype	Significance	ClinVar
1-45584165-G-A		not specified	Uncertain significance (Mar 07, 2025)
1-45584198-G-C		not specified	Uncertain significance (Oct 27, 2021)
1-45591233-G-A		not specified	Uncertain significance (Mar 13, 2023)
1-45591246-C-G		not specified	Uncertain significance (Apr 10, 2023)
1-45602289-G-T		not specified	Uncertain significance (Aug 21, 2024)
1-45602304-C-T		not specified	Uncertain significance (Nov 08, 2021)
1-45602338-A-G		not specified	Uncertain significance (Mar 25, 2024)
1-45604961-A-G		not specified	Uncertain significance (Jun 06, 2023)
1-45606511-T-G		not specified	Uncertain significance (Jan 05, 2022)
1-45606585-A-G		not specified	Uncertain significance (Jan 27, 2025)
1-45607358-C-A		not specified	Uncertain significance (Mar 12, 2024)
1-45607378-A-C		not specified	Uncertain significance (Aug 02, 2023)
1-45607416-G-A		not specified	Uncertain significance (Feb 10, 2022)
1-45607437-A-G		not specified	Uncertain significance (Aug 13, 2021)
1-45607438-G-A		not specified	Uncertain significance (Dec 04, 2024)
1-45607438-G-T		not specified	Uncertain significance (Jul 27, 2024)
1-45607475-A-G		not specified	Uncertain significance (Jul 14, 2023)
1-45607496-A-C			Benign (Jul 23, 2018)
1-45607552-A-G		not specified	Uncertain significance (Feb 22, 2023)
1-45607576-C-T		not specified	Likely benign (Nov 17, 2022)
1-45607621-C-T		not specified	Uncertain significance (May 31, 2023)
1-45607623-G-C		not specified	Uncertain significance (Dec 17, 2021)
1-45607669-A-C		not specified	Uncertain significance (Oct 29, 2021)
1-45607672-G-A		not specified	Likely benign (Feb 05, 2024)
1-45607694-G-T		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NASP	protein_coding	protein_coding	ENST00000350030	15	35049

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00447	125742	0	4	125746	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.606	368	402	0.915	0.0000193	5114
Missense in Polyphen		69	114.09	0.60478		1517
Synonymous	-0.279	151	147	1.03	0.00000776	1495
Loss of Function	4.96	5	38.0	0.131	0.00000162	530

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000922	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for DNA replication, normal cell cycle progression and cell proliferation. Forms a cytoplasmic complex with HSP90 and H1 linker histones and stimulates HSP90 ATPase activity. NASP and H1 histone are subsequently released from the complex and translocate to the nucleus where the histone is released for binding to DNA. {ECO:0000250|UniProtKB:Q99MD9}.

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.118
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.56

Haploinsufficiency Scores

• pHI: 0.829
• hipred: N
• hipred_score: 0.328
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.982

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nasp
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;blastocyst development;DNA replication;DNA replication-dependent nucleosome assembly;DNA replication-independent nucleosome assembly;cell population proliferation;male gonad development;protein transport;response to testosterone;CENP-A containing nucleosome assembly;histone exchange
• Cellular component: nuclear chromatin;nucleus;nucleoplasm;cytoplasm;protein-containing complex
• Molecular function: protein binding;histone binding