NT5DC1

protein-coding

5'-nucleotidase domain containing 1

Gene summary

While the exact function of the protein encoded by this gene is not known, it belongs to the 5'(3')-deoxyribonucleotidase family. [provided by RefSeq, May 2010]

Previous symbols:

NT5C2L1

MANE transcript

NM_152729.3

Inheritance

—

ClinVar variants

U:76B:2

Top phenotype

Metaphyseal chondrodysplasia, Schmid type

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr6:116,100,851-116,249,497

External References & Databases

Ensembl (ENSG00000178425)

Transcript & Mutation Effects

hg38 • Region Span ~148.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NT5DC1 variants in ClinVar

8 Conditions Cataloged

not providedTotal: 407

Metaphyseal chondrodysplasia, Schmid typeTotal: 144

Inborn genetic diseasesTotal: 137

not specifiedTotal: 123

COL10A1-related disorderTotal: 23

COL10A1-related disordersTotal: 17

Nager syndromeTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152729.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			74 clinvar	2 clinvar		76
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	76	2	0	78

Highest pathogenic variant AF is 0.0000049576

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152729.3	RefSeq	NP_689942.2	12	MANE Select
ENST00000319550.9	Ensembl	ENSP00000326858.3	12	MANE Select
ENST00000419791.3	Ensembl	ENSP00000393578.1	7	Standard
ENST00000460749.1	Ensembl	ENSP00000433238.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

dephosphorylation

Molecular Function

5'-nucleotidase activity
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000319550
Coding exons: 12
Length: 148649
Individuals with no LoFs: 125707
Homozygous LoFs: 0
Heterozygous LoFs: 41
Defined: 125748
p: 0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.535	212	235	0.902	0.0000112	2983
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00016	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000061	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00019	0.00018	rare
South Asian	0.00030	0.00029	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0989

Intolerance Scores

LoFtool: 0.821
RVIS EVS: -0.03
RVIS percentile EVS: 51.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.233

Gene Damage Prediction

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