PNMA3

PNMA family member 3, the group of Paraneoplastic Ma antigens

Basic information

Region (hg38): X:153056408-153060467

Links

ENSG00000183837 ∙ NCBI:29944 ∙ OMIM:300675 ∙ HGNC:18742 ∙ Uniprot:Q9UL41 ∙ 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 PNMA3 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNMA3 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						0
missense			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	1	0

Variants in PNMA3

This is a list of pathogenic ClinVar variants found in the PNMA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-153058067-G-A		not specified	Uncertain significance (Apr 06, 2023)
X-153058205-C-T		not specified	Uncertain significance (Dec 06, 2022)
X-153058211-C-T		not specified	Uncertain significance (Feb 05, 2024)
X-153058232-C-G		not specified	Uncertain significance (Sep 15, 2021)
X-153058263-G-C		not specified	Uncertain significance (Nov 15, 2021)
X-153058284-G-A		not specified	Uncertain significance (Mar 22, 2023)
X-153058385-G-A		not specified	Likely benign (Dec 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PNMA3	protein_coding	protein_coding	ENST00000447306	1	4062

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.747	167	196	0.850	0.0000162	2979
Missense in Polyphen		36	46.563	0.77314		777
Synonymous	1.06	66	77.9	0.847	0.00000607	985
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.573
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.96

Haploinsufficiency Scores

• pHI: 0.195
• hipred: N
• hipred_score: 0.206
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pnma3

Gene ontology

• Biological process: positive regulation of apoptotic process
• Cellular component: nucleolus
• Molecular function: nucleic acid binding;zinc ion binding