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GeneBe

ROM1

retinal outer segment membrane protein 1, the group of Tetraspanins

Basic information

Region (hg38): 11:62611721-62615116

Links

ENSG00000149489NCBI:6094OMIM:180721HGNC:10254Uniprot:Q03395AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • retinitis pigmentosa (Supportive), mode of inheritance: AD
  • retinitis pigmentosa 7 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Retinitis pigmentosa 7, digenicDigenicGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic8202715; 1684223
Digenic inheritance (with PRPH2) has been described

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ROM1 gene.

  • not provided (276 variants)
  • Retinitis pigmentosa (36 variants)
  • Inborn genetic diseases (14 variants)
  • not specified (6 variants)
  • Retinitis pigmentosa 7 (4 variants)
  • Retinal dystrophy (3 variants)
  • Retinitis pigmentosa 7, digenic (2 variants)
  • Larsen-like syndrome, B3GAT3 type (2 variants)
  • Retinitis Pigmentosa, Dominant (1 variants)
  • Macular dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ROM1 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
3
clinvar
63
clinvar
3
clinvar
69
missense
161
clinvar
3
clinvar
1
clinvar
165
nonsense
4
clinvar
1
clinvar
5
start loss
1
clinvar
1
frameshift
10
clinvar
1
clinvar
11
inframe indel
6
clinvar
6
splice donor/acceptor (+/-2bp)
0
splice region
1
2
3
non coding
5
clinvar
10
clinvar
15
Total 0 0 190 78 4

Variants in ROM1

This is a list of pathogenic ClinVar variants found in the ROM1 region.

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

Position Type Phenotype Significance ClinVar
11-62612451-C-A not specified Uncertain significance (Nov 10, 2022)2325445
11-62612451-C-T not specified Uncertain significance (Oct 05, 2021)2230463
11-62612740-C-T Retinitis pigmentosa Uncertain significance (Jan 13, 2018)879335
11-62612755-G-A Retinitis pigmentosa Uncertain significance (Jan 13, 2018)879336
11-62612783-G-C Retinitis pigmentosa Uncertain significance (Jan 13, 2018)305150
11-62612787-G-T Retinitis pigmentosa Uncertain significance (Jan 13, 2018)305151
11-62612788-G-A Retinitis pigmentosa Likely benign (Jan 13, 2018)305152
11-62612797-AG-A Retinitis Pigmentosa, Dominant Uncertain significance (Jun 14, 2016)305153
11-62612800-G-C Retinitis pigmentosa Likely benign (Jan 13, 2018)305154
11-62612844-G-A Retinitis pigmentosa Benign (Jan 13, 2018)305155
11-62612953-G-T Retinitis pigmentosa Benign (Jan 12, 2018)305156
11-62612981-C-T Retinitis pigmentosa Uncertain significance (Jan 12, 2018)305157
11-62613045-G-T Retinitis pigmentosa Uncertain significance (Jan 13, 2018)880525
11-62613122-CA-C Retinitis Pigmentosa, Dominant Uncertain significance (Jun 14, 2016)305158
11-62613164-G-C Retinitis pigmentosa Uncertain significance (Jan 12, 2018)305159
11-62613255-C-T Retinitis pigmentosa Uncertain significance (Jan 13, 2018)305160
11-62613282-A-AT Uncertain significance (Jul 19, 2022)2096363
11-62613289-C-T Uncertain significance (Jul 05, 2022)1481775
11-62613290-G-A Retinal dystrophy Likely benign (Oct 01, 2023)3028223
11-62613290-G-T Likely benign (Jul 26, 2022)1611808
11-62613291-G-A Uncertain significance (Dec 10, 2023)2702112
11-62613296-G-T Uncertain significance (Dec 24, 2021)2058925
11-62613296-GC-G Uncertain significance (Aug 10, 2023)1942158
11-62613297-C-T Uncertain significance (Aug 01, 2022)1711318
11-62613301-T-G Uncertain significance (Jun 13, 2022)1005092

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ROM1protein_codingprotein_codingENST00000278833 33399
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0004120.86512508346591257460.00264
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.9062331971.180.00001212175
Missense in Polyphen9973.5111.3467884
Synonymous-0.68010192.71.090.00000549824
Loss of Function1.33712.00.5856.96e-7110

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.02800.0280
Ashkenazi Jewish0.002780.00278
East Asian0.002990.00299
Finnish0.00004640.0000462
European (Non-Finnish)0.0002060.000202
Middle Eastern0.002990.00299
South Asian0.004730.00232
Other0.001010.000815

dbNSFP

Source: dbNSFP

Function
FUNCTION: May function as an adhesion molecule involved in stabilization and compaction of outer segment disks or in the maintenance of the curvature of the rim. It is essential for disk morphogenesis.;

Recessive Scores

pRec
0.230

Intolerance Scores

loftool
0.639
rvis_EVS
-0.22
rvis_percentile_EVS
37.43

Haploinsufficiency Scores

pHI
0.411
hipred
N
hipred_score
0.144
ghis
0.573

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.108

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rom1
Phenotype
nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);

Gene ontology

Biological process
cell adhesion;cell surface receptor signaling pathway;visual perception;regulation of gene expression;camera-type eye photoreceptor cell differentiation;retina vasculature development in camera-type eye
Cellular component
integral component of plasma membrane;photoreceptor outer segment membrane
Molecular function