NT5DC1

5'-nucleotidase domain containing 1

Basic information

Region (hg38): 6:116100850-116249497

Previous symbols: [ "NT5C2L1" ]

Links

ENSG00000178425 ∙ NCBI:221294 ∙ ∙ HGNC:21556 ∙ Uniprot:Q5TFE4 ∙ 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 NT5DC1 gene.

• not provided (268 variants)
• Metaphyseal chondrodysplasia, Schmid type (108 variants)
• Inborn genetic diseases (50 variants)
• not specified (12 variants)
• Metaphyseal chondrodysplasia (8 variants)
• COL10A1-related condition (5 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NT5DC1 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			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	19	21	192	74	34	340
Total	19	21	206	76	34

Highest pathogenic variant AF is 0.00000658

Variants in NT5DC1

This is a list of pathogenic ClinVar variants found in the NT5DC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-116100970-G-A		not specified	Uncertain significance (Feb 02, 2022)
6-116106274-G-A		not specified	Uncertain significance (Apr 07, 2022)
6-116106308-A-G		not specified	Likely benign (Feb 06, 2023)
6-116108380-T-A		not specified	Uncertain significance (Oct 10, 2023)
6-116108400-C-A		not specified	Uncertain significance (Jan 03, 2024)
6-116110896-G-T		not specified	Uncertain significance (Dec 21, 2023)
6-116110943-G-A		not specified	Uncertain significance (Aug 31, 2022)
6-116115711-A-C		not specified	Uncertain significance (Dec 06, 2021)
6-116115750-G-A		not specified	Uncertain significance (Sep 17, 2021)
6-116117886-A-G		not specified	Uncertain significance (Nov 29, 2021)
6-116117897-G-A		not specified	Uncertain significance (Sep 26, 2023)
6-116117904-T-C		not specified	Uncertain significance (Aug 30, 2022)
6-116118928-T-C		Metaphyseal chondrodysplasia, Schmid type	Uncertain significance (Jan 13, 2018)
6-116118967-C-T		Metaphyseal chondrodysplasia, Schmid type	Benign (Jan 13, 2018)
6-116118988-C-T		Metaphyseal chondrodysplasia, Schmid type	Uncertain significance (Jan 13, 2018)
6-116119031-T-C		Metaphyseal chondrodysplasia, Schmid type	Benign (Jan 13, 2018)
6-116119035-G-A		Metaphyseal chondrodysplasia, Schmid type	Uncertain significance (Jan 13, 2018)
6-116119047-C-T		Metaphyseal chondrodysplasia, Schmid type	Benign (Jan 12, 2018)
6-116119048-G-A		Metaphyseal chondrodysplasia, Schmid type	Benign (Jan 13, 2018)
6-116119173-C-T		Metaphyseal chondrodysplasia, Schmid type	Uncertain significance (Jan 12, 2018)
6-116119240-A-G		Metaphyseal chondrodysplasia	Likely benign (Jun 14, 2016)
6-116119283-A-C		Metaphyseal chondrodysplasia, Schmid type	Benign (Jan 13, 2018)
6-116119399-T-C		Metaphyseal chondrodysplasia, Schmid type	Uncertain significance (Jan 13, 2018)
6-116119420-A-G		Metaphyseal chondrodysplasia, Schmid type	Benign (Jan 13, 2018)
6-116119501-A-G		Metaphyseal chondrodysplasia, Schmid type	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NT5DC1	protein_coding	protein_coding	ENST00000319550	12	148649

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.14e-7	0.964	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.535	212	235	0.902	0.0000112	2983
Missense in Polyphen		42	57.351	0.73233		789
Synonymous	0.689	77	85.1	0.905	0.00000418	820
Loss of Function	1.99	14	24.7	0.568	0.00000111	319

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000407	0.000406
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000607	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.0000607	0.0000544
South Asian	0.000299	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0989

Intolerance Scores

• loftool: 0.821
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.477
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.233

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nt5dc1

Gene ontology

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