POLR2M

RNA polymerase II subunit M, the group of RNA polymerase subunits

Basic information

Region (hg38): 15:57706694-57782762

Previous symbols: [ "GRINL1A" ]

Links

ENSG00000255529 ∙ NCBI:81488 ∙ OMIM:606485 ∙ HGNC:14862 ∙ Uniprot:P0CAP2, Q6EEV4 ∙ 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 POLR2M gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POLR2M 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				2	1	3
missense			32	5	2	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	0	0	32	7	6

Variants in POLR2M

This is a list of pathogenic ClinVar variants found in the POLR2M region.

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

Position	Type	Phenotype	Significance	ClinVar
15-57706858-C-G		not specified	Uncertain significance (Jan 22, 2024)
15-57706867-G-C		not specified	Uncertain significance (Apr 13, 2023)
15-57706929-G-T		not specified	Uncertain significance (Apr 07, 2022)
15-57706942-C-G		not specified	Uncertain significance (Jul 11, 2023)
15-57707106-G-C			Benign (Jun 19, 2021)
15-57707277-C-G			Benign (Jun 19, 2021)
15-57708783-C-T			Benign (Jun 09, 2021)
15-57708784-A-G		not specified	Likely benign (Apr 11, 2023)
15-57708788-C-T		not specified	Uncertain significance (Feb 10, 2022)
15-57708830-C-T		not specified	Uncertain significance (Apr 15, 2022)
15-57708887-C-T		not specified	Uncertain significance (Jan 02, 2024)
15-57708892-A-G		not specified	Uncertain significance (Jan 03, 2024)
15-57709103-C-G		not specified	Uncertain significance (Jun 21, 2021)
15-57709109-A-G		not specified	Uncertain significance (Apr 13, 2022)
15-57709126-C-T		not specified	Uncertain significance (Jul 25, 2023)
15-57709142-C-T		not specified	Uncertain significance (Feb 23, 2023)
15-57709150-A-G		not specified	Uncertain significance (Dec 14, 2023)
15-57709205-C-T		not specified	Uncertain significance (Aug 02, 2022)
15-57709237-G-A		not specified	Likely benign (Dec 20, 2021)
15-57709278-G-T		not specified	Uncertain significance (Mar 06, 2023)
15-57709291-T-C		not specified	Uncertain significance (Feb 24, 2023)
15-57709311-G-A		not specified	Uncertain significance (Jun 16, 2023)
15-57709355-A-G		not specified	Uncertain significance (Dec 17, 2023)
15-57711988-C-G		Inborn genetic diseases	Uncertain significance (Oct 26, 2021)
15-57712028-G-A		Inborn genetic diseases	Uncertain significance (Sep 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POLR2M	protein_coding	protein_coding	ENST00000299638	4	190730

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0311	0.960	125669	0	8	125677	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.845	240	206	1.17	0.0000112	2406
Missense in Polyphen		66	62.234	1.0605		800
Synonymous	-0.266	81	78.0	1.04	0.00000421	713
Loss of Function	2.30	5	14.4	0.347	7.58e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000458	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.154

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Polr2m

Gene ontology

• Biological process: RNA biosynthetic process;intracellular signal transduction;maintenance of ER location
• Cellular component: nuclear envelope;RNA polymerase II, holoenzyme;neuronal cell body
• Molecular function: DNA-directed 5'-3' RNA polymerase activity