PRAM1

PML-RARA regulated adaptor molecule 1

Basic information

Region (hg38): 19:8490056-8502640

Links

ENSG00000133246 ∙ NCBI:84106 ∙ OMIM:606466 ∙ HGNC:30091 ∙ Uniprot:Q96QH2 ∙ 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 PRAM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRAM1 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	2	5
missense			62	2	4	68
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	62	5	6

Variants in PRAM1

This is a list of pathogenic ClinVar variants found in the PRAM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-8490205-A-T		not specified	Uncertain significance (Oct 25, 2024)
19-8490224-G-T		not specified	Uncertain significance (Apr 13, 2022)
19-8490355-T-A		not specified	Uncertain significance (Sep 30, 2024)
19-8490362-C-T		not specified	Uncertain significance (Jan 24, 2025)
19-8490494-C-T		not specified	Uncertain significance (May 15, 2024)
19-8490656-A-G		not specified	Uncertain significance (Mar 04, 2024)
19-8490693-C-T		not specified	Uncertain significance (Aug 12, 2024)
19-8490694-G-A			Likely benign (Jan 01, 2023)
19-8490696-G-A		not specified	Uncertain significance (Sep 26, 2022)
19-8490698-C-T		not specified	Uncertain significance (May 10, 2024)
19-8490913-C-T		not specified	Uncertain significance (Jan 24, 2024)
19-8490958-T-C		not specified	Uncertain significance (Jan 03, 2024)
19-8490960-G-C		not specified	Uncertain significance (Mar 25, 2024)
19-8490977-C-G		not specified	Uncertain significance (Oct 06, 2024)
19-8490990-T-C		not specified	Uncertain significance (Oct 26, 2022)
19-8491105-C-T		not specified	Likely benign (Jun 16, 2023)
19-8491134-C-A		not specified	Uncertain significance (Jan 27, 2022)
19-8497814-T-C		not specified	Uncertain significance (Jan 08, 2025)
19-8498238-G-A		not specified	Uncertain significance (Aug 12, 2021)
19-8498259-A-G		not specified	Uncertain significance (Jan 07, 2022)
19-8498283-C-T		not specified	Uncertain significance (May 10, 2024)
19-8498411-A-G		not specified	Uncertain significance (Sep 13, 2023)
19-8498418-C-T		not specified	Uncertain significance (Apr 08, 2022)
19-8498480-G-A		not specified	Uncertain significance (Oct 02, 2023)
19-8498504-G-A		not specified	Uncertain significance (Nov 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRAM1	protein_coding	protein_coding	ENST00000423345	10	13057

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000300	0.997	124735	0	46	124781	0.000184

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.107	420	426	0.985	0.0000282	4252
Missense in Polyphen		115	128.12	0.89762		1488
Synonymous	-0.0174	200	200	1.00	0.0000153	1383
Loss of Function	2.64	10	24.0	0.417	0.00000117	296

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000361	0.000273
Ashkenazi Jewish	0.00	0.00
East Asian	0.000182	0.000167
Finnish	0.000148	0.0000928
European (Non-Finnish)	0.000220	0.000212
Middle Eastern	0.000182	0.000167
South Asian	0.000394	0.000261
Other	0.000351	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in myeloid differentiation. May be involved in integrin signaling in neutrophils. Binds to PtdIns(4)P.
• Pathway: regulation of transcriptional activity by pml (Consensus)

Recessive Scores

• pRec: 0.0941

Intolerance Scores

• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.24

Haploinsufficiency Scores

• pHI: 0.0721
• hipred: N
• hipred_score: 0.169
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.759

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pram1
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: integrin-mediated signaling pathway;regulation of neutrophil degranulation;T cell receptor signaling pathway;protein localization to plasma membrane
• Cellular component: plasma membrane;protein-containing complex
• Molecular function: protein binding;lipid binding;protein kinase binding