R3HDM4

R3H domain containing 4

Basic information

Region (hg38): 19:896502-913245

Previous symbols: [ "C19orf22" ]

Links

ENSG00000198858 ∙ NCBI:91300 ∙ ∙ HGNC:28270 ∙ Uniprot:Q96D70 ∙ 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 R3HDM4 gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the R3HDM4 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						0
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in R3HDM4

This is a list of pathogenic ClinVar variants found in the R3HDM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-897460-C-T		not specified	Uncertain significance (Jan 04, 2024)
19-897480-G-A		not specified	Uncertain significance (Nov 12, 2021)
19-897533-G-C		not specified	Uncertain significance (Jan 05, 2022)
19-899641-C-T		not specified	Uncertain significance (Jul 26, 2021)
19-900126-G-C		not specified	Uncertain significance (Jul 06, 2022)
19-900144-C-T		not specified	Uncertain significance (Aug 02, 2023)
19-900835-T-C		not specified	Uncertain significance (Aug 30, 2021)
19-900855-G-T		not specified	Uncertain significance (Nov 01, 2022)
19-900867-C-G		not specified	Uncertain significance (Sep 01, 2021)
19-900873-T-C		not specified	Uncertain significance (Feb 10, 2023)
19-900886-C-T		not specified	Uncertain significance (Nov 21, 2022)
19-900897-T-A		not specified	Uncertain significance (Dec 15, 2023)
19-901436-C-T		not specified	Uncertain significance (Oct 03, 2022)
19-901451-C-T		not specified	Uncertain significance (Sep 15, 2021)
19-901453-G-A		not specified	Uncertain significance (Jun 22, 2023)
19-901511-C-T		not specified	Likely benign (Jan 17, 2023)
19-901514-C-T		not specified	Uncertain significance (Dec 16, 2023)
19-913100-C-A		not specified	Uncertain significance (Apr 12, 2022)
19-913105-G-A		not specified	Uncertain significance (Mar 20, 2023)
19-913113-C-A		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
R3HDM4	protein_coding	protein_coding	ENST00000361574	8	16738

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000463	0.880	125565	1	31	125597	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.532	177	158	1.12	0.0000112	1679
Missense in Polyphen		66	68.924	0.95757		632
Synonymous	-1.36	82	67.8	1.21	0.00000442	566
Loss of Function	1.38	7	12.2	0.573	5.97e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000155	0.000154
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000239	0.000231
European (Non-Finnish)	0.000178	0.000159
Middle Eastern	0.0000544	0.0000544
South Asian	0.000101	0.0000980
Other	0.000171	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.325
• ghis: 0.529

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	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: R3hdm4

Gene ontology

• Cellular component: nucleus
• Molecular function: nucleic acid binding