ROM1

retinal outer segment membrane protein 1, the group of Tetraspanins

Basic information

Region (hg38): 11:62611721-62615116

Links

ENSG00000149489

∙ NCBI:6094 ∙ OMIM:180721 ∙ HGNC:10254 ∙ Uniprot:Q03395 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 7, digenic	Digenic	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	8202715; 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 (268 variants)
Retinitis pigmentosa (48 variants)
Inborn genetic diseases (12 variants)
not specified (6 variants)
Retinitis pigmentosa 7 (4 variants)
Retinitis Pigmentosa, Dominant (3 variants)
Retinal dystrophy (3 variants)
Retinitis pigmentosa 7, digenic (2 variants)
Larsen-like syndrome, B3GAT3 type (2 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	50		53
missense			152	23	4	179
nonsense			7	1		8
start loss						0
frameshift			14	2		16
inframe indel			4			4
splice variant			2	3		5
non coding			12	12	3	27
Total	0	0	194	91	7

Variants in ROM1

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

Position	Phenotype	Significance	ClinVar
11-62612451-C-A	Inborn genetic diseases	Uncertain significance (Nov 10, 2022)	link
11-62612451-C-T	Inborn genetic diseases	Uncertain significance (Oct 05, 2021)	link
11-62612740-C-T	Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)	link
11-62612755-G-A	Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)	link
11-62612783-G-C	Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)	link
11-62612787-G-T	Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)	link
11-62612788-G-A	Retinitis pigmentosa	Likely benign (Jan 13, 2018)	link
11-62612797-AG-A	Retinitis Pigmentosa, Dominant	Uncertain significance (Jun 14, 2016)	link
11-62612800-G-C	Retinitis pigmentosa	Likely benign (Jan 13, 2018)	link
11-62612844-G-A	Retinitis pigmentosa	Benign (Jan 13, 2018)	link
11-62612953-G-T	Retinitis pigmentosa	Benign (Jan 12, 2018)	link
11-62612981-C-T	Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)	link
11-62613045-G-T	Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)	link
11-62613122-CA-C	Retinitis Pigmentosa, Dominant	Uncertain significance (Jun 14, 2016)	link
11-62613164-G-C	Retinitis pigmentosa	Uncertain significance (Jan 12, 2018)	link
11-62613255-C-T	Retinitis pigmentosa	Uncertain significance (Jan 13, 2018)	link
11-62613282-A-AT		Uncertain significance (Jul 19, 2022)	link
11-62613289-C-T		Uncertain significance (Jul 05, 2022)	link
11-62613290-G-T		Likely benign (Jul 26, 2022)	link
11-62613296-G-T		Uncertain significance (Dec 24, 2021)	link
11-62613296-GC-G		Uncertain significance (May 29, 2022)	link
11-62613297-C-T		Uncertain significance (Aug 01, 2022)	link
11-62613301-T-G		Uncertain significance (Jun 13, 2022)	link
11-62613310-C-G		Uncertain significance (May 19, 2022)	link
11-62613311-C-T		Likely benign (Apr 07, 2022)	link

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ROM1	protein_coding	protein_coding	ENST00000278833	3	3399

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000412	0.865	125083	4	659	125746	0.00264

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.906	233	197	1.18	0.0000121	2175
Missense in Polyphen		99	73.511	1.3467		884
Synonymous	-0.680	101	92.7	1.09	0.00000549	824
Loss of Function	1.33	7	12.0	0.585	6.96e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0280	0.0280
Ashkenazi Jewish	0.00278	0.00278
East Asian	0.00299	0.00299
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000206	0.000202
Middle Eastern	0.00299	0.00299
South Asian	0.00473	0.00232
Other	0.00101	0.000815

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

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

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