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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 54.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_002482.4	NP_002473.2	15	yes	-
ENST00000350030.8	ENSP00000255120.5	15	yes	-
NM_152298.4	NP_689511.2	14	-	-
NM_001195193.2	NP_001182122.1	13	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• not_specified (96 variants)
• not_provided (3 variants)

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. These statistics are base on transcript: NM_002482.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	1	1	5
missense			92	11		103
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7			7
Total	0	0	102	12	1

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
		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

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

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