TMEM98

transmembrane protein 98

Basic information

Region (hg38): 17:32927910-32945106

Links

ENSG00000006042 ∙ NCBI:26022 ∙ OMIM:615949 ∙ HGNC:24529 ∙ Uniprot:Q9Y2Y6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nanophthalmos 4 (Strong), mode of inheritance: AD
• nanophthalmia (Supportive), mode of inheritance: AD
• nanophthalmos 4 (Moderate), mode of inheritance: AD
• nanophthalmos 4 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nanophthalmos 4	AD	Ophthalmologic	As the condition can include glaucoma, surveillance can allow early interventions that may potentially be beneficial related to preservation of visual status	Ophthalmologic	24852644

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMEM98 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM98 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				2	1	3
missense			10		1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	10	2	3

Variants in TMEM98

This is a list of pathogenic ClinVar variants found in the TMEM98 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-32931541-G-T		Inborn genetic diseases	Uncertain significance (Apr 26, 2023)
17-32931625-C-T		Inborn genetic diseases	Uncertain significance (Jun 16, 2023)
17-32931646-C-T		Inborn genetic diseases	Uncertain significance (Oct 12, 2022)
17-32931668-G-C		TMEM98-related disorder	Benign (Jan 03, 2020)
17-32933209-A-C		Inborn genetic diseases	Uncertain significance (Sep 14, 2022)
17-32933217-C-A		Inborn genetic diseases	Uncertain significance (Dec 12, 2023)
17-32933275-TGGAGAATGAAGACTGGATCGAAGATGCCTCGTAA-T		Nanophthalmos 4	Pathogenic (Mar 10, 2016)
17-32933289-T-C			Benign (Jun 26, 2018)
17-32936412-C-T		TMEM98-related disorder	Likely benign (Aug 08, 2019)
17-32936425-G-A		Inborn genetic diseases	Uncertain significance (Jan 24, 2024)
17-32936435-G-A		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
17-32939478-G-A		Inborn genetic diseases	Uncertain significance (Feb 16, 2023)
17-32939495-G-T		Inborn genetic diseases	Uncertain significance (Nov 20, 2023)
17-32939499-A-C		Inborn genetic diseases	Uncertain significance (Mar 29, 2024)
17-32939523-C-T		Inborn genetic diseases	Uncertain significance (Jun 27, 2022)
17-32939531-C-T		TMEM98-related disorder	Likely benign (Feb 10, 2021)
17-32939532-G-A		Inborn genetic diseases	Uncertain significance (Mar 20, 2024)
17-32940816-C-T			Benign (Dec 01, 2023)
17-32940889-G-C		Nanophthalmos 4	Pathogenic (Aug 01, 2014)
17-32940899-A-C		Nanophthalmos 4	Pathogenic (Mar 10, 2016)
17-32940922-G-A		Inborn genetic diseases	Uncertain significance (May 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM98	protein_coding	protein_coding	ENST00000579849	6	17197

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0119	0.955	125739	0	8	125747	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.728	110	134	0.823	0.00000755	1441
Missense in Polyphen		5	10.355	0.48285		114
Synonymous	0.152	53	54.4	0.974	0.00000325	474
Loss of Function	1.85	5	11.9	0.421	7.54e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000453	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.000105	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.493
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.166
• hipred: N
• hipred_score: 0.441
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.406

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem98
• Phenotype: growth/size/body region phenotype

Gene ontology

• Cellular component: endoplasmic reticulum;integral component of membrane