TMEM79

transmembrane protein 79

Basic information

Region (hg38): 1:156282935-156293185

Links

ENSG00000163472 ∙ NCBI:84283 ∙ OMIM:615531 ∙ HGNC:28196 ∙ Uniprot:Q9BSE2 ∙ 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 TMEM79 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM79 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	2	4
missense			39	3	1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	5	3

Variants in TMEM79

This is a list of pathogenic ClinVar variants found in the TMEM79 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-156285279-C-T		not specified	Likely benign (Aug 17, 2022)
1-156285287-A-G		not specified	Uncertain significance (Jan 30, 2024)
1-156285294-C-T		not specified	Uncertain significance (Dec 26, 2023)
1-156285318-G-A			Benign (May 14, 2018)
1-156285438-G-T		not specified	Uncertain significance (Jun 29, 2022)
1-156285444-C-T		not specified	Uncertain significance (Jan 09, 2024)
1-156285486-C-T		not specified	Uncertain significance (Sep 17, 2021)
1-156285494-G-C		not specified	Uncertain significance (Sep 22, 2022)
1-156285600-C-T		not specified	Uncertain significance (Jan 27, 2022)
1-156285625-C-G		not specified	Uncertain significance (May 31, 2023)
1-156285627-T-G		not specified	Uncertain significance (Aug 23, 2021)
1-156285668-C-T			Likely benign (May 09, 2018)
1-156285679-A-G			Likely benign (May 09, 2018)
1-156285689-G-A		not specified	Uncertain significance (Jun 07, 2024)
1-156285707-C-T		not specified	Uncertain significance (Jul 09, 2021)
1-156285747-G-T		not specified	Uncertain significance (Jul 05, 2023)
1-156285761-G-A		not specified	Uncertain significance (Nov 01, 2022)
1-156285780-C-A		not specified	Uncertain significance (Jul 25, 2023)
1-156285794-G-A		not specified	Uncertain significance (May 05, 2022)
1-156285798-G-C		not specified	Uncertain significance (Jun 22, 2024)
1-156285809-C-T		not specified	Uncertain significance (Feb 03, 2022)
1-156285810-G-A		not specified	Uncertain significance (Dec 21, 2023)
1-156285840-G-A		not specified	Uncertain significance (Jan 10, 2023)
1-156285844-C-G			Benign (May 14, 2018)
1-156285853-T-G		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM79	protein_coding	protein_coding	ENST00000405535	3	10251

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000439	0.638	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.416	264	246	1.07	0.0000154	2470
Missense in Polyphen		108	90.132	1.1982		912
Synonymous	-0.395	113	108	1.05	0.00000674	900
Loss of Function	0.961	10	13.9	0.721	7.71e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000450	0.000449
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.000218	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000241	0.000237
Middle Eastern	0.000218	0.000217
South Asian	0.000555	0.000555
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Contributes to the epidermal integrity and skin barrier function. Plays a role in the lamellar granule (LG) secretory system and in the stratum corneum (SC) epithelial cell formation (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.793
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.59

Haploinsufficiency Scores

• pHI: 0.279
• hipred: N
• hipred_score: 0.248
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.602

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem79
• Phenotype: vision/eye phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); pigmentation phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: epithelial cell maturation;hair follicle morphogenesis;cuticle development;regulated exocytosis;positive regulation of epidermis development;establishment of skin barrier;cornification
• Cellular component: lysosomal membrane;integral component of membrane;trans-Golgi network membrane
• Molecular function: protein binding;identical protein binding