ASNSD1

asparagine synthetase domain containing 1

Basic information

Region (hg38): 2:189661385-189670831

Links

ENSG00000138381 ∙ NCBI:54529 ∙ OMIM:619739 ∙ HGNC:24910 ∙ Uniprot:Q9NWL6 ∙ 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 ASNSD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASNSD1 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						0
missense			31	3		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	31	4	0

Variants in ASNSD1

This is a list of pathogenic ClinVar variants found in the ASNSD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-189661607-C-T			Likely benign (Dec 01, 2022)
2-189666245-T-C		not specified	Uncertain significance (Oct 03, 2022)
2-189666289-G-A		not specified	Uncertain significance (Feb 06, 2023)
2-189666418-T-C		not specified	Uncertain significance (Apr 18, 2024)
2-189666493-T-C		not specified	Uncertain significance (Feb 10, 2023)
2-189666594-C-G		not specified	Uncertain significance (Nov 09, 2022)
2-189666620-C-T		not specified	Uncertain significance (Apr 05, 2023)
2-189666652-C-G		not specified	Uncertain significance (Oct 13, 2023)
2-189666661-G-C		not specified	Uncertain significance (Mar 01, 2023)
2-189666717-A-T		not specified	Uncertain significance (May 29, 2024)
2-189666769-A-G		not specified	Uncertain significance (Apr 23, 2024)
2-189666802-G-T		not specified	Uncertain significance (Feb 21, 2024)
2-189666934-G-A		not specified	Uncertain significance (Nov 14, 2023)
2-189667061-A-G		not specified	Likely benign (Mar 14, 2023)
2-189667154-G-A		not specified	Uncertain significance (May 31, 2024)
2-189667177-A-G		not specified	Uncertain significance (Dec 28, 2023)
2-189667181-A-G		not specified	Uncertain significance (Jan 06, 2023)
2-189667207-G-A		not specified	Likely benign (Mar 24, 2023)
2-189667291-A-G		not specified	Uncertain significance (Nov 07, 2023)
2-189667310-C-G		not specified	Uncertain significance (Sep 16, 2021)
2-189667480-C-T		not specified	Likely benign (Sep 01, 2021)
2-189667510-A-G		not specified	Uncertain significance (Oct 12, 2021)
2-189667546-G-T		not specified	Uncertain significance (Feb 23, 2023)
2-189667580-A-G		not specified	Uncertain significance (Dec 16, 2022)
2-189667801-C-T		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASNSD1	protein_coding	protein_coding	ENST00000260952	3	9447

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.25e-17	0.00479	125611	0	137	125748	0.000545

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.530	312	339	0.919	0.0000176	4217
Missense in Polyphen		115	124.76	0.92179		1435
Synonymous	0.0477	116	117	0.994	0.00000541	1267
Loss of Function	-0.204	24	22.9	1.05	0.00000134	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00106	0.00105
Ashkenazi Jewish	0.00	0.00
East Asian	0.000382	0.000381
Finnish	0.000462	0.000462
European (Non-Finnish)	0.000698	0.000695
Middle Eastern	0.000382	0.000381
South Asian	0.000331	0.000327
Other	0.000816	0.000815

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0900

Intolerance Scores

• loftool: 0.933
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.44

Haploinsufficiency Scores

• pHI: 0.0512
• hipred: N
• hipred_score: 0.219
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.658

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Asnsd1

Gene ontology

• Biological process: asparagine biosynthetic process;glutamine metabolic process;biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function;asparagine synthase (glutamine-hydrolyzing) activity