NAALADL2

N-acetylated alpha-linked acidic dipeptidase like 2, the group of MicroRNA protein coding host genes|M28 metallopeptidases

Basic information

Region (hg38): 3:174438572-175810548

Links

ENSG00000177694 ∙ NCBI:254827 ∙ OMIM:608806 ∙ HGNC:23219 ∙ Uniprot:Q58DX5 ∙ 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 NAALADL2 gene.

• Inborn genetic diseases (31 variants)
• not provided (3 variants)
• Developmental cataract (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAALADL2 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			30	2	1	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	30	4	1

Variants in NAALADL2

This is a list of pathogenic ClinVar variants found in the NAALADL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-175096823-A-G		not specified	Uncertain significance (Aug 30, 2021)
3-175096841-A-T		not specified	Uncertain significance (Jun 24, 2022)
3-175096975-T-G		not specified	Uncertain significance (Jul 19, 2023)
3-175097003-C-A		not specified	Uncertain significance (Dec 20, 2023)
3-175097034-G-T		not specified	Uncertain significance (Feb 10, 2022)
3-175097101-C-T		not specified	Uncertain significance (Feb 01, 2023)
3-175097108-A-G		not specified	Uncertain significance (Dec 18, 2023)
3-175097119-G-A			Likely benign (May 01, 2023)
3-175097135-G-A		not specified	Uncertain significance (Oct 10, 2023)
3-175097135-G-T		not specified	Uncertain significance (Mar 07, 2024)
3-175097171-T-C		not specified	Uncertain significance (Oct 26, 2021)
3-175097239-T-C		not specified	Uncertain significance (May 27, 2022)
3-175097267-C-G		not specified	Uncertain significance (Jul 12, 2023)
3-175097272-G-C		not specified	Uncertain significance (Oct 03, 2023)
3-175097283-G-C		not specified	Uncertain significance (Feb 13, 2024)
3-175233944-C-G		NAALADL2-related disorder	Likely benign (May 20, 2022)
3-175233952-A-C		not specified	Uncertain significance (Apr 13, 2022)
3-175233984-T-C		not specified	Uncertain significance (Dec 05, 2022)
3-175233990-C-T		not specified	Uncertain significance (Aug 10, 2023)
3-175234070-A-G		not specified	Uncertain significance (Dec 17, 2021)
3-175234078-G-A		NAALADL2-related disorder	Likely benign (Nov 16, 2023)
3-175234093-T-A		not specified	Uncertain significance (Oct 05, 2023)
3-175234212-G-T		NAALADL2-related disorder	Likely benign (Nov 28, 2023)
3-175256423-G-A		not specified	Uncertain significance (Aug 02, 2021)
3-175256457-G-C		not specified	Uncertain significance (Feb 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAALADL2	protein_coding	protein_coding	ENST00000454872	14	1367066

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.73e-8	0.999	124480	0	159	124639	0.000638

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.82	506	403	1.25	0.0000202	5164
Missense in Polyphen		114	108.8	1.0478		1384
Synonymous	-1.26	166	147	1.13	0.00000769	1512
Loss of Function	2.95	18	37.5	0.480	0.00000201	475

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000950	0.000949
Ashkenazi Jewish	0.000827	0.000795
East Asian	0.000279	0.000278
Finnish	0.000514	0.000511
European (Non-Finnish)	0.000966	0.000956
Middle Eastern	0.000279	0.000278
South Asian	0.000197	0.000196
Other	0.000520	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be catalytically inactive.

Intolerance Scores

• loftool: 0.903
• rvis_EVS: 1.34
• rvis_percentile_EVS: 94.29

Haploinsufficiency Scores

• pHI: 0.206
• hipred: N
• hipred_score: 0.195

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.166

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Naaladl2

Gene ontology

• Biological process: response to bacterium
• Cellular component: nucleoplasm;integral component of membrane
• Molecular function: protein binding