NEPRO

nucleolus and neural progenitor protein

Basic information

Region (hg38): 3:113002444-113019861

Previous symbols: [ "C3orf17" ]

Links

ENSG00000163608 ∙ NCBI:25871 ∙ OMIM:617089 ∙ HGNC:24496 ∙ Uniprot:Q6NW34 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• anauxetic dysplasia (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Anauxetic dysplasia 3	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	26633546; 29620724; 31250547

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NEPRO gene.

• Anauxetic dysplasia 3 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEPRO 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				2	2	4
missense	1		6	2	3	12
nonsense						0
start loss						0
frameshift			1			1
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	1	0	7	6	6

Variants in NEPRO

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

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

Position	Type	Phenotype	Significance	ClinVar
3-113005531-A-G		NEPRO-related disorder	Likely benign (May 08, 2019)
3-113005711-C-A		Abnormal cerebral white matter morphology;Microcephaly	Uncertain significance (May 12, 2021)
3-113005866-C-T		NEPRO-related disorder	Benign (Jul 01, 2024)
3-113005886-GT-G		NEPRO-related disorder	Uncertain significance (Dec 05, 2022)
3-113008202-G-A		NEPRO-related disorder	Uncertain significance (Mar 27, 2024)
3-113008238-C-T		Abnormal cerebral white matter morphology;Microcephaly	Uncertain significance (May 12, 2021)
3-113008337-A-T		Anauxetic dysplasia 3	Benign (Jul 14, 2021)
3-113008375-G-T		NEPRO-related disorder	Benign (Apr 24, 2019)
3-113008427-TCTC-T		NEPRO-related disorder	Likely benign (Mar 30, 2018)
3-113010697-T-C		NEPRO-related disorder	Benign (Oct 28, 2019)
3-113011069-C-T			Likely benign (Aug 01, 2024)
3-113011087-C-T		NEPRO-related disorder	Uncertain significance (Jul 27, 2023)
3-113011106-C-G		NEPRO-related disorder	Uncertain significance (Oct 27, 2023)
3-113011333-C-T		not specified	Uncertain significance (Aug 17, 2021)
3-113013310-C-G		Anauxetic dysplasia 3	Pathogenic (May 09, 2022)
3-113013348-C-T		NEPRO-related disorder	Benign (May 01, 2023)
3-113014014-G-A		Anauxetic dysplasia 3	Uncertain significance (Mar 14, 2024)
3-113017466-G-A		NEPRO-related disorder	Likely benign (Jul 23, 2019)
3-113019471-C-T		Anauxetic dysplasia 3	Benign (Jul 14, 2021)
3-113019557-G-A		NEPRO-related disorder	Benign (Oct 28, 2019)
3-113019564-C-T		NEPRO-related disorder	Likely benign (Nov 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEPRO	protein_coding	protein_coding	ENST00000314400	9	17422

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.01e-8	0.877	125574	0	174	125748	0.000692

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0895	299	295	1.01	0.0000144	3728
Missense in Polyphen		85	92.646	0.91747		1219
Synonymous	1.17	91	106	0.856	0.00000519	1046
Loss of Function	1.68	16	25.1	0.638	0.00000114	340

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00274	0.00272
Ashkenazi Jewish	0.00	0.00
East Asian	0.00141	0.00141
Finnish	0.000835	0.000832
European (Non-Finnish)	0.000570	0.000554
Middle Eastern	0.00141	0.00141
South Asian	0.000377	0.000359
Other	0.000827	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in cortex development as part of the Notch signaling pathway. Downstream of Notch may repress the expression of proneural genes and inhibit neuronal differentiation thereby maintaining neural progenitors. May also play a role in preimplentation embryo development. {ECO:0000250|UniProtKB:Q8R2U2}.

Recessive Scores

• pRec: 0.0708

Intolerance Scores

• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.3

Haploinsufficiency Scores

• pHI: 0.0666
• hipred: N
• hipred_score: 0.145
• ghis: 0.493

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Nepro
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cellular phenotype

Gene ontology

• Biological process: negative regulation of neuron differentiation;positive regulation of Notch signaling pathway
• Cellular component: nucleus;nucleolus