PNMA2

PNMA family member 2, the group of Paraneoplastic Ma antigens

Basic information

Region (hg38): 8:26504701-26514092

Links

ENSG00000240694 ∙ NCBI:10687 ∙ OMIM:603970 ∙ HGNC:9159 ∙ Uniprot:Q9UL42 ∙ 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 PNMA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNMA2 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			6			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	6	0	0

Variants in PNMA2

This is a list of pathogenic ClinVar variants found in the PNMA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-26507674-T-C		not specified	Uncertain significance (Dec 01, 2022)
8-26507711-G-A		not specified	Uncertain significance (May 30, 2023)
8-26507761-C-T		not specified	Uncertain significance (Oct 10, 2023)
8-26507774-T-A		not specified	Uncertain significance (Nov 27, 2024)
8-26507778-C-A		not specified	Uncertain significance (Nov 10, 2022)
8-26507866-T-G		not specified	Uncertain significance (Aug 14, 2023)
8-26508734-C-A		not specified	Uncertain significance (Nov 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PNMA2	protein_coding	protein_coding	ENST00000522362	1	9407

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00157	0.893	124504	0	27	124531	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.292	204	216	0.944	0.0000130	2342
Missense in Polyphen		44	47.261	0.93099		626
Synonymous	0.585	84	91.1	0.922	0.00000554	750
Loss of Function	1.41	6	11.0	0.543	6.22e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000511	0.000511
Ashkenazi Jewish	0.000100	0.0000993
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000810	0.0000808
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.758
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.0629
• hipred: N
• hipred_score: 0.259
• ghis: 0.576

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.926

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pnma2

Gene ontology

• Biological process: positive regulation of apoptotic process
• Cellular component: nucleolus
• Molecular function: protein binding