R3HCC1L

protein-coding

R3H domain and coiled-coil containing 1 like

Gene summary

Located in exon-exon junction complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C10orf28

MANE transcript

NM_001351015.2

Inheritance

—

ClinVar variants

U:138B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr10:98,134,624-98,244,897

External References & Databases

Ensembl (ENSG00000166024)

Transcript & Mutation Effects

hg38 • Region Span ~110.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to R3HCC1L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 141

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001351015.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			135 clinvar	12 clinvar		147
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	138	12	0	150

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 144 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001351015.2	RefSeq	NP_001337944.2	6	MANE Select
ENST00000298999.8	Ensembl	ENSP00000298999.3	6	MANE Select
NM_001256619.2	RefSeq	NP_001243548.2	7	Standard
NM_001256620.2	RefSeq	NP_001243549.2	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Molecular Function

protein binding

Cellular Component

exon-exon junction complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000298999
Coding exons: 6
Length: 110268
Individuals with no LoFs: 125649
Homozygous LoFs: 0
Heterozygous LoFs: 82
Defined: 125731
p: 0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.736	453	411	1.10	0.0000205	5154
Missense (PolyPhen)		96	102.33	0.93812		1269
Synonymous	-1.49	167	144	1.16	0.00000743	1480
Loss of Function	1.57	18	26.8	0.673	0.00000146	362

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00063	0.00062	rare
South Asian	0.000099	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0701

Intolerance Scores

RVIS EVS: 3.29
RVIS percentile EVS: 99.41

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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