NANP

protein-coding

N-acetylneuraminic acid phosphatase, the group of HAD Asp-based non-protein phosphatases|Haloacid dehalogenase like hydrolase domain containing

Gene summary

Enables N-acylneuraminate-9-phosphatase activity. Involved in CMP-N-acetylneuraminate biosynthetic process and N-acetylneuraminate biosynthetic process. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C20orf147
HDHD4

MANE transcript

NM_152667.3

Inheritance

—

ClinVar variants

U:31B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr20:25,612,935-25,624,014

External References & Databases

Ensembl (ENSG00000170191)

Transcript & Mutation Effects

hg38 • Region Span ~11.1 kb

Loading mutation effect viewer...

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 NANP variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 32

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152667.3. 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			30 clinvar	2 clinvar		32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	31	2	0	33

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152667.3	RefSeq	NP_689880.1	2	MANE Select
ENST00000304788.4	Ensembl	ENSP00000302441.3	2	MANE Select
ENST00001133609.1	Ensembl	ENSP00000805564.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Amino sugar and nucleotide sugar metabolism - Homo sapiens (human)
Sialuria or French Type Sialuria
Sialuria or French Type Sialuria
Amino Sugar Metabolism
G(M2)-Gangliosidosis: Variant B, Tay-sachs disease

Biological Process

carbohydrate metabolic process
N-acetylglucosamine biosynthetic process
dephosphorylation
N-acetylneuraminate biosynthetic process

Molecular Function

N-acylneuraminate-9-phosphatase activity

Cellular Component

cellular_component
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000304788
Coding exons: 2
Length: 11241
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125748
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.560	120	139	0.866	0.00000704	1611
Missense (PolyPhen)		40	42.929	0.93177		525
Synonymous	-1.23	65	53.6	1.21	0.00000300	480
Loss of Function	0.471	7	8.48	0.826	4.21e-7	113

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000051	0.000046	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.171

Intolerance Scores

LoFtool: 0.514
RVIS EVS: -0.4
RVIS percentile EVS: 26.53

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.694

Gene Damage Prediction

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