TMEM19

transmembrane protein 19

Basic information

Region (hg38): 12:71686082-71705047

Links

ENSG00000139291 ∙ NCBI:55266 ∙ ∙ HGNC:25605 ∙ Uniprot:Q96HH6 ∙ 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 TMEM19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM19 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						0
missense			13	1	2	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	2

Variants in TMEM19

This is a list of pathogenic ClinVar variants found in the TMEM19 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-71689653-G-A		not specified	Uncertain significance (Dec 26, 2023)
12-71689681-T-A		not specified	Uncertain significance (Jan 26, 2023)
12-71696462-A-T		not specified	Uncertain significance (Aug 12, 2022)
12-71696495-A-T		not specified	Uncertain significance (May 06, 2022)
12-71696504-T-A			Benign (Feb 20, 2018)
12-71697351-A-G		not specified	Uncertain significance (Apr 26, 2024)
12-71697424-T-C		not specified	Uncertain significance (Jun 26, 2023)
12-71697432-G-T		not specified	Uncertain significance (Nov 08, 2022)
12-71697433-C-T		not specified	Uncertain significance (Nov 08, 2022)
12-71697509-A-G		not specified	Uncertain significance (May 10, 2022)
12-71698932-G-A		not specified	Uncertain significance (Jan 24, 2024)
12-71698975-T-A		not specified	Uncertain significance (Jun 05, 2024)
12-71699051-A-T		not specified	Uncertain significance (Oct 12, 2022)
12-71699094-A-G		not specified	Uncertain significance (Dec 13, 2023)
12-71700846-A-G		not specified	Uncertain significance (Oct 03, 2022)
12-71700847-C-G			Benign (Feb 20, 2018)
12-71700862-A-G		not specified	Likely benign (Feb 17, 2024)
12-71700910-A-T		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM19	protein_coding	protein_coding	ENST00000266673	6	17970

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00520	0.972	125658	0	90	125748	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.417	164	180	0.912	0.00000887	2156
Missense in Polyphen		40	59.766	0.66928		718
Synonymous	-0.297	72	68.9	1.05	0.00000369	698
Loss of Function	1.99	6	14.0	0.428	6.91e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00140	0.00138
Ashkenazi Jewish	0.00	0.00
East Asian	0.00126	0.00125
Finnish	0.00	0.00
European (Non-Finnish)	0.000365	0.000360
Middle Eastern	0.00126	0.00125
South Asian	0.0000334	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.217
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.0797
• hipred: N
• hipred_score: 0.350
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem19

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding