R3HDM2

R3H domain containing 2

Basic information

Region (hg38): 12:57253762-57431043

Links

ENSG00000179912 ∙ NCBI:22864 ∙ OMIM:619886 ∙ HGNC:29167 ∙ Uniprot:Q9Y2K5 ∙ 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 R3HDM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the R3HDM2 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	1
missense			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	1

Variants in R3HDM2

This is a list of pathogenic ClinVar variants found in the R3HDM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57254840-C-T		not specified	Uncertain significance (Dec 20, 2023)
12-57254933-G-A		not specified	Uncertain significance (Oct 30, 2023)
12-57254973-C-A		not specified	Uncertain significance (Feb 10, 2022)
12-57254990-C-A		not specified	Uncertain significance (Mar 07, 2024)
12-57255016-C-G		not specified	Uncertain significance (Aug 02, 2021)
12-57255041-G-A		not specified	Uncertain significance (Mar 15, 2024)
12-57256424-G-A		not specified	Uncertain significance (Mar 04, 2024)
12-57256446-G-A		not specified	Uncertain significance (Dec 13, 2022)
12-57256482-G-A		not specified	Uncertain significance (Sep 16, 2021)
12-57258023-T-A		not specified	Uncertain significance (Sep 28, 2022)
12-57258952-A-G		not specified	Uncertain significance (Feb 11, 2022)
12-57266789-G-A			Benign (Sep 19, 2018)
12-57268325-G-C		not specified	Uncertain significance (Jul 08, 2022)
12-57268430-C-T		not specified	Uncertain significance (May 01, 2024)
12-57269016-G-A		not specified	Uncertain significance (Jun 29, 2023)
12-57269017-G-C		not specified	Uncertain significance (Mar 01, 2024)
12-57269059-G-T		not specified	Uncertain significance (Oct 12, 2022)
12-57269071-T-A		not specified	Uncertain significance (Jan 23, 2023)
12-57269391-G-A		not specified	Uncertain significance (Jun 05, 2024)
12-57269394-C-T		not specified	Uncertain significance (Dec 19, 2022)
12-57269922-A-G		not specified	Uncertain significance (Jun 04, 2024)
12-57269933-G-A		not specified	Uncertain significance (May 29, 2024)
12-57269977-G-T		not specified	Uncertain significance (Jul 14, 2022)
12-57269994-C-G		not specified	Uncertain significance (Jun 06, 2023)
12-57280401-G-A		not specified	Uncertain significance (Aug 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
R3HDM2	protein_coding	protein_coding	ENST00000347140	22	181397

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000484	125743	0	3	125746	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.33	321	538	0.597	0.0000288	6422
Missense in Polyphen		58	147.57	0.39304		2009
Synonymous	2.33	155	197	0.788	0.0000102	1881
Loss of Function	6.16	4	51.9	0.0771	0.00000253	575

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000341	0.0000341
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000887	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.0829
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.06

Haploinsufficiency Scores

• pHI: 0.387
• hipred: Y
• hipred_score: 0.631
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.773

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: R3hdm2

Gene ontology

• Cellular component: nucleus
• Molecular function: RNA binding