NT5DC4

5'-nucleotidase domain containing 4

Basic information

Region (hg38): 2:112721020-112742879

Links

ENSG00000144130 ∙ NCBI:284958 ∙ ∙ HGNC:27678 ∙ Uniprot:Q86YG4 ∙ 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 NT5DC4 gene.

• Filippi syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NT5DC4 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
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1		19	10	11	41
Total	1	0	19	11	11

Variants in NT5DC4

This is a list of pathogenic ClinVar variants found in the NT5DC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-112722760-C-G			Likely benign (Feb 01, 2023)
2-112738554-A-T			Benign (Nov 10, 2018)
2-112738863-G-A			Uncertain significance (Jul 09, 2022)
2-112738875-C-T			Benign (Jan 22, 2024)
2-112738876-G-A		not specified	Benign (Jan 29, 2024)
2-112738887-C-T		Inborn genetic diseases	Uncertain significance (Jul 05, 2024)
2-112738888-A-T			Uncertain significance (Jul 12, 2022)
2-112738942-G-T		Inborn genetic diseases	Uncertain significance (Jan 03, 2022)
2-112738943-T-A			Benign (Jul 25, 2022)
2-112738945-C-G		Inborn genetic diseases	Uncertain significance (Feb 06, 2024)
2-112738950-A-G			Uncertain significance (Sep 01, 2022)
2-112738970-C-T			Likely benign (Mar 01, 2024)
2-112738977-C-T			Benign (Nov 01, 2024)
2-112738989-G-A		Inborn genetic diseases	Uncertain significance (Oct 21, 2021)
2-112738991-C-T			Likely benign (Sep 29, 2023)
2-112738995-C-T		Filippi syndrome	Uncertain significance (Sep 01, 2021)
2-112738998-C-T		Inborn genetic diseases	Uncertain significance (Mar 01, 2023)
2-112739003-A-G			Benign (Jan 15, 2024)
2-112739008-T-C		Inborn genetic diseases	Uncertain significance (Mar 20, 2023)
2-112739034-G-A			Uncertain significance (Dec 10, 2023)
2-112739055-G-T		CKAP2L-related disorder	Benign (Dec 07, 2023)
2-112739377-T-A			Benign (Jun 20, 2021)
2-112740760-C-T			Benign (Nov 10, 2018)
2-112740806-G-A			Likely benign (Oct 17, 2023)
2-112740822-G-A		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NT5DC4	protein_coding	protein_coding	ENST00000327581	17	21394

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.78e-9	0.921	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.616	213	240	0.888	0.0000132	2801
Missense in Polyphen		45	56.663	0.79417		835
Synonymous	1.11	80	93.6	0.854	0.00000533	780
Loss of Function	1.84	17	27.4	0.620	0.00000124	330

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

Recessive Scores

• pRec: 0.0966

Haploinsufficiency Scores

• pHI: 0.0982

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0439

Gene Damage Prediction

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

Gene ontology

• Biological process: dephosphorylation
• Molecular function: 5'-nucleotidase activity;metal ion binding