PRIMA1

proline rich membrane anchor 1

Basic information

Region (hg38): 14:93718297-93788485

Links

ENSG00000175785 ∙ NCBI:145270 ∙ OMIM:613851 ∙ HGNC:18319 ∙ Uniprot:Q86XR5 ∙ 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 PRIMA1 gene.

• Sleep-related hypermotor epilepsy (122 variants)
• Inborn genetic diseases (7 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRIMA1 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				27	5	32
missense			62			62
nonsense			1			1
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			2	9		11
non coding			1	17	1	19
Total	0	0	65	44	6

Variants in PRIMA1

This is a list of pathogenic ClinVar variants found in the PRIMA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-93721451-A-G		Sleep-related hypermotor epilepsy	Uncertain significance (Aug 20, 2021)
14-93721455-C-G		Sleep-related hypermotor epilepsy	Uncertain significance (Dec 02, 2022)
14-93721455-C-T		Sleep-related hypermotor epilepsy	Uncertain significance (Jun 09, 2022)
14-93721456-G-A		Sleep-related hypermotor epilepsy	Likely benign (May 20, 2023)
14-93721462-C-T		Sleep-related hypermotor epilepsy	Likely benign (Mar 14, 2020)
14-93721464-C-T		Sleep-related hypermotor epilepsy	Uncertain significance (Nov 27, 2023)
14-93721465-G-A		Sleep-related hypermotor epilepsy	Likely benign (Jul 04, 2022)
14-93721465-G-T		Sleep-related hypermotor epilepsy	Uncertain significance (Jun 12, 2019)
14-93721466-T-C		not specified	Uncertain significance (May 01, 2022)
14-93721473-C-T		Sleep-related hypermotor epilepsy	Uncertain significance (Aug 30, 2021)
14-93721475-T-C		Sleep-related hypermotor epilepsy	Uncertain significance (Mar 25, 2022)
14-93721480-G-C		Sleep-related hypermotor epilepsy • not specified	Uncertain significance (Nov 18, 2022)
14-93721486-C-T		Sleep-related hypermotor epilepsy	Benign (Feb 01, 2024)
14-93721487-G-A		Sleep-related hypermotor epilepsy	Uncertain significance (Jul 14, 2023)
14-93721498-G-C		Sleep-related hypermotor epilepsy	Likely benign (Mar 04, 2022)
14-93721504-C-T		Sleep-related hypermotor epilepsy • PRIMA1-related disorder	Benign/Likely benign (Jan 21, 2024)
14-93721508-G-A		Sleep-related hypermotor epilepsy	Uncertain significance (Feb 02, 2022)
14-93721512-C-T		Sleep-related hypermotor epilepsy	Uncertain significance (Jul 17, 2023)
14-93721513-G-A		Sleep-related hypermotor epilepsy	Likely benign (Nov 18, 2023)
14-93721519-G-A		Sleep-related hypermotor epilepsy	Likely benign (May 11, 2023)
14-93721523-T-C		Sleep-related hypermotor epilepsy	Uncertain significance (Nov 29, 2022)
14-93721527-C-T		Sleep-related hypermotor epilepsy	Uncertain significance (Aug 31, 2022)
14-93721528-G-A		Sleep-related hypermotor epilepsy	Likely benign (Jan 28, 2024)
14-93721540-T-C		Sleep-related hypermotor epilepsy	Likely benign (Apr 15, 2023)
14-93721541-G-A		Sleep-related hypermotor epilepsy	Uncertain significance (Jul 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRIMA1	protein_coding	protein_coding	ENST00000393140	4	70184

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.629	0.365	125245	0	2	125247	0.00000798

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.976	63	88.9	0.709	0.00000515	960
Missense in Polyphen		21	33.313	0.63039		346
Synonymous	0.754	31	36.8	0.842	0.00000249	313
Loss of Function	2.18	1	7.42	0.135	3.94e-7	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required to anchor acetylcholinesterase (ACHE) to the basal lamina of the neuromuscular junction and to the membrane of neuronal synapses in brain. Also able to organize ACHE into tetramers (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.159

Intolerance Scores

• loftool: 0.129
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.172
• hipred: N
• hipred_score: 0.208
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.198

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prima1
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: neurotransmitter catabolic process
• Cellular component: plasma membrane;integral component of membrane;cell junction;synapse
• Molecular function: protein membrane anchor