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.

• not_specified (41 variants)
• not_provided (2 variants)

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. These statistics are base on transcript: NM_000018279.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			40	1	2	43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	40	1	2

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