NAALAD2

N-acetylated alpha-linked acidic dipeptidase 2, the group of M28 metallopeptidases

Basic information

Region (hg38): 11:90131515-90192894

Links

ENSG00000077616 ∙ NCBI:10003 ∙ OMIM:611636 ∙ HGNC:14526 ∙ Uniprot:Q9Y3Q0 ∙ 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 NAALAD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAALAD2 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			40	2		42
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	3	0

Variants in NAALAD2

This is a list of pathogenic ClinVar variants found in the NAALAD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-90134774-G-A		not specified	Uncertain significance (Jun 07, 2024)
11-90134784-A-G		not specified	Uncertain significance (Feb 15, 2023)
11-90135600-C-T		not specified	Uncertain significance (Jul 05, 2023)
11-90135601-G-A		not specified	Uncertain significance (Jul 31, 2023)
11-90135619-G-A		not specified	Uncertain significance (Feb 03, 2022)
11-90135661-C-T		not specified	Uncertain significance (Dec 21, 2023)
11-90147413-T-C		not specified	Uncertain significance (May 17, 2023)
11-90147464-C-A		not specified	Uncertain significance (Dec 14, 2021)
11-90147485-A-C		not specified	Uncertain significance (Apr 28, 2022)
11-90147491-C-T		not specified	Uncertain significance (Mar 29, 2022)
11-90147496-G-A		not specified	Uncertain significance (Dec 15, 2022)
11-90149043-G-A		not specified	Uncertain significance (Feb 07, 2023)
11-90149060-A-T		not specified	Uncertain significance (Mar 28, 2023)
11-90149097-G-A		not specified	Uncertain significance (Aug 09, 2021)
11-90150485-G-C		not specified	Uncertain significance (Feb 05, 2024)
11-90150510-G-A		not specified	Uncertain significance (Jan 31, 2024)
11-90150510-G-T		not specified	Uncertain significance (Mar 20, 2024)
11-90150546-G-A		not specified	Uncertain significance (Feb 23, 2023)
11-90152308-C-T		not specified	Uncertain significance (Oct 27, 2023)
11-90152327-A-G		not specified	Uncertain significance (May 31, 2023)
11-90152353-C-A		not specified	Uncertain significance (Mar 29, 2022)
11-90152412-G-A		not specified	Uncertain significance (Feb 06, 2023)
11-90158171-G-C		not specified	Uncertain significance (Mar 05, 2024)
11-90158186-C-T		not specified	Uncertain significance (May 01, 2022)
11-90158237-C-T		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAALAD2	protein_coding	protein_coding	ENST00000534061	19	61380

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.43e-20	0.0364	125542	2	204	125748	0.000819

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.474	359	385	0.932	0.0000186	4828
Missense in Polyphen		145	163.52	0.88677		2027
Synonymous	0.334	126	131	0.963	0.00000603	1387
Loss of Function	1.07	35	42.6	0.822	0.00000208	546

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00216	0.00215
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.00206	0.00185
Finnish	0.000462	0.000462
European (Non-Finnish)	0.000628	0.000598
Middle Eastern	0.00206	0.00185
South Asian	0.00106	0.00101
Other	0.00132	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has N-acetylated-alpha-linked-acidic dipeptidase (NAALADase) activity. Also exhibits a dipeptidyl-peptidase IV type activity. Inactivate the peptide neurotransmitter N- acetylaspartylglutamate. {ECO:0000269|PubMed:10085079}.
• Pathway: Metabolism of amino acids and derivatives;Metabolism;Amino acid synthesis and interconversion (transamination) (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.969
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.04

Haploinsufficiency Scores

• pHI: 0.189
• hipred: N
• hipred_score: 0.187
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.136

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Naalad2

Gene ontology

• Biological process: proteolysis;cellular amino acid biosynthetic process;neurotransmitter catabolic process
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: carboxypeptidase activity;serine-type peptidase activity;metallopeptidase activity;dipeptidyl-peptidase activity;dipeptidase activity;metal ion binding;N-formylglutamate deformylase activity