PNMA5

PNMA family member 5, the group of Paraneoplastic Ma antigens

Basic information

Region (hg38): X:152988824-152994116

Links

ENSG00000198883 ∙ NCBI:114824 ∙ OMIM:300916 ∙ HGNC:18743 ∙ Uniprot:Q96PV4 ∙ 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 PNMA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNMA5 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					3	3
missense			11	3	1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	3	4

Variants in PNMA5

This is a list of pathogenic ClinVar variants found in the PNMA5 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-152990274-T-C		not specified	Uncertain significance (Mar 16, 2022)
X-152990287-C-T		not specified	Uncertain significance (Oct 09, 2024)
X-152990295-G-A		not specified	Uncertain significance (Feb 19, 2025)
X-152990296-C-T		not specified	Uncertain significance (Feb 19, 2025)
X-152990308-A-C		not specified	Uncertain significance (Oct 03, 2023)
X-152990316-C-G		not specified	Uncertain significance (Dec 14, 2024)
X-152990347-T-A			Benign (Mar 29, 2018)
X-152990364-G-A		not specified	Uncertain significance (Aug 20, 2024)
X-152990391-C-T		not specified	Likely benign (Dec 07, 2024)
X-152990406-C-T		not specified	Uncertain significance (Apr 01, 2024)
X-152990425-G-A		not specified	Uncertain significance (Jun 23, 2023)
X-152990440-G-T		not specified	Uncertain significance (Jul 09, 2024)
X-152990446-C-T		not specified	Uncertain significance (Dec 19, 2023)
X-152990471-G-T		not specified	Likely benign (Nov 26, 2024)
X-152990474-G-C		not specified	Uncertain significance (Dec 12, 2024)
X-152990494-C-T		not specified	Uncertain significance (Dec 22, 2024)
X-152990554-G-A		not specified	Uncertain significance (Nov 10, 2024)
X-152990658-C-G		not specified	Uncertain significance (Dec 28, 2023)
X-152990660-C-A			Benign (Jul 05, 2018)
X-152990699-G-A			Benign (Jul 06, 2018)
X-152990703-G-A		not specified	Uncertain significance (Aug 08, 2023)
X-152990912-G-A			Benign (Jul 06, 2018)
X-152991547-T-C			Likely benign (Oct 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PNMA5	protein_coding	protein_coding	ENST00000439251	1	5304

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	0.480	155	173	0.897	0.0000134	2899
Missense in Polyphen		40	48.447	0.82564		885
Synonymous	1.20	55	67.6	0.814	0.00000520	916
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

Intolerance Scores

• loftool: 0.802
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.0733
• hipred: N
• hipred_score: 0.112
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0247

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pnma5

Gene ontology

• Biological process: positive regulation of apoptotic process
• Molecular function: protein binding;identical protein binding