HNRNPM

heterogeneous nuclear ribonucleoprotein M, the group of Heterogeneous nuclear ribonucleoproteins|RNA binding motif containing

Basic information

Region (hg38): 19:8444767-8489114

Previous symbols: [ "NAGR1", "HNRPM" ]

Links

ENSG00000099783 ∙ NCBI:4670 ∙ OMIM:160994 ∙ HGNC:5046 ∙ Uniprot:P52272 ∙ 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 HNRNPM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPM 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				1	3	4
missense			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	31	1	3

Variants in HNRNPM

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

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

Position	Type	Phenotype	Significance	ClinVar
19-8445021-C-T		not specified	Uncertain significance (Jul 05, 2023)
19-8445029-G-A		not specified	Uncertain significance (May 31, 2023)
19-8445039-C-A		not specified	Uncertain significance (Mar 29, 2023)
19-8445057-A-C		not specified	Uncertain significance (Aug 21, 2023)
19-8445074-G-A		Long QT syndrome	Likely benign (-)
19-8445104-C-T		not specified	Uncertain significance (Feb 06, 2023)
19-8455419-C-T		not specified	Uncertain significance (Nov 03, 2022)
19-8455467-A-G		not specified	Uncertain significance (Dec 01, 2023)
19-8463625-A-G		not specified	Uncertain significance (Aug 13, 2021)
19-8465338-A-T		not specified	Uncertain significance (Jan 03, 2024)
19-8465385-T-C		not specified	Uncertain significance (Dec 07, 2021)
19-8465426-C-T		not specified	Uncertain significance (Dec 02, 2022)
19-8465448-A-G		not specified	Uncertain significance (Jan 31, 2024)
19-8467537-A-G		not specified	Uncertain significance (May 30, 2024)
19-8468767-C-G			Benign (Jul 04, 2018)
19-8468817-G-T		not specified	Uncertain significance (Oct 05, 2023)
19-8471408-G-C		not specified	Uncertain significance (Jul 25, 2023)
19-8474177-G-A			Benign (Jul 04, 2018)
19-8485690-C-T		not specified	Uncertain significance (Feb 17, 2024)
19-8485716-G-A		not specified	Uncertain significance (Mar 07, 2024)
19-8485768-T-C		not specified	Uncertain significance (Sep 06, 2022)
19-8485774-G-T		not specified	Uncertain significance (Feb 26, 2024)
19-8485819-A-G		not specified	Uncertain significance (Nov 08, 2022)
19-8485822-T-C		not specified	Uncertain significance (Aug 14, 2023)
19-8485872-G-A		not specified	Uncertain significance (Apr 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HNRNPM	protein_coding	protein_coding	ENST00000325495	16	44348

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000114	125643	0	2	125645	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.74	300	467	0.643	0.0000303	4801
Missense in Polyphen		44	102.34	0.42995		1145
Synonymous	-1.15	175	157	1.12	0.0000111	1394
Loss of Function	5.24	0	32.0	0.00	0.00000180	373

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000381	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Pre-mRNA binding protein in vivo, binds avidly to poly(G) and poly(U) RNA homopolymers in vitro. Involved in splicing. Acts as a receptor for carcinoembryonic antigen in Kupffer cells, may initiate a series of signaling events leading to tyrosine phosphorylation of proteins and induction of IL-1 alpha, IL-6, IL-10 and tumor necrosis factor alpha cytokines.
• Pathway: Spliceosome - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in squamous cell - TarBase;mRNA Processing;FGFR2 alternative splicing;Signaling by FGFR2;Signal Transduction;Signaling by FGFR;Metabolism of RNA;mRNA Splicing - Major Pathway;Signaling by Receptor Tyrosine Kinases;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• loftool: 0.374
• rvis_EVS: -1.4
• rvis_percentile_EVS: 4.22

Haploinsufficiency Scores

• pHI: 0.104
• hipred: Y
• hipred_score: 0.748
• ghis: 0.666

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.944

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hnrnpm

Gene ontology

• Biological process: alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;fibroblast growth factor receptor signaling pathway;RNA metabolic process;regulation of mRNA stability involved in response to oxidative stress
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;nucleolus;cytoplasm;membrane;nuclear matrix;paraspeckles;collagen-containing extracellular matrix;extracellular exosome;catalytic step 2 spliceosome;post-mRNA release spliceosomal complex;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA binding;protein binding;protein domain specific binding