NAALADL1

N-acetylated alpha-linked acidic dipeptidase like 1, the group of M28 metallopeptidases

Basic information

Region (hg38): 11:65044818-65058553

Links

ENSG00000168060 ∙ NCBI:10004 ∙ OMIM:602640 ∙ HGNC:23536 ∙ Uniprot:Q9UQQ1 ∙ 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 NAALADL1 gene.

• not_specified (132 variants)
• Retinal_dystrophy (15 variants)
• Optic_atrophy (3 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAALADL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005468.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			136	8		144
nonsense			1			1
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)		1				1
Total	0	1	138	8	0

Highest pathogenic variant AF is 0.000087119864

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAALADL1	protein_coding	protein_coding	ENST00000358658	18	13732

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.82e-21	0.00568	125563	0	185	125748	0.000736

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.170	447	457	0.978	0.0000281	4721
Missense in Polyphen		124	133.28	0.93036		1313
Synonymous	1.34	169	193	0.877	0.0000122	1565
Loss of Function	0.544	34	37.6	0.904	0.00000184	404

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00211	0.00211
Ashkenazi Jewish	0.00	0.00
East Asian	0.00126	0.00120
Finnish	0.00228	0.00227
European (Non-Finnish)	0.000484	0.000475
Middle Eastern	0.00126	0.00120
South Asian	0.000393	0.000359
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: NAALADase-like activity unknown. Has no NAAG hydrolyzing activity. Exhibits a dipeptidyl-peptidase IV type activity. In vitro, cleaves Gly-Pro-AMC (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.957
• rvis_EVS: -1.01
• rvis_percentile_EVS: 8.16

Haploinsufficiency Scores

• pHI: 0.0714
• hipred: N
• hipred_score: 0.170
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.178

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Naaladl1

Gene ontology

• Biological process: proteolysis
• Cellular component: integral component of membrane;apical plasma membrane
• Molecular function: carboxypeptidase activity;peptidase activity;metallopeptidase activity;dipeptidase activity;metal ion binding