TM4SF19

transmembrane 4 L six family member 19

Basic information

Region (hg38): 3:196319342-196338503

Links

ENSG00000145107 ∙ NCBI:116211 ∙ ∙ HGNC:25167 ∙ Uniprot:Q96DZ7 ∙ 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 TM4SF19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM4SF19 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
missense			18	1		19
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	20	3	0

Variants in TM4SF19

This is a list of pathogenic ClinVar variants found in the TM4SF19 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-196320042-A-C			Likely benign (Sep 01, 2023)
3-196320048-T-G			Likely benign (Sep 01, 2023)
3-196323730-T-C		not specified	Uncertain significance (Dec 20, 2023)
3-196323775-G-A		not specified	Likely benign (May 15, 2024)
3-196323809-T-C		not specified	Uncertain significance (Sep 27, 2022)
3-196323856-G-A		not specified	Uncertain significance (Jan 19, 2024)
3-196323891-G-A		not specified	Likely benign (Nov 06, 2023)
3-196323912-C-T		not specified	Likely benign (Jun 11, 2024)
3-196323913-G-A		not specified	Uncertain significance (Nov 03, 2023)
3-196323990-G-C		not specified	Uncertain significance (Nov 21, 2023)
3-196324313-T-C		not specified	Uncertain significance (Mar 20, 2024)
3-196326959-C-T		not specified	Uncertain significance (Feb 10, 2022)
3-196326992-C-G		not specified	Uncertain significance (Jan 23, 2024)
3-196327032-C-A		not specified	Uncertain significance (Jul 09, 2021)
3-196327413-C-T		not specified	Uncertain significance (Aug 02, 2021)
3-196327464-C-T		not specified	Uncertain significance (Mar 22, 2023)
3-196327466-T-A		not specified	Uncertain significance (Feb 05, 2024)
3-196327503-C-G		not specified	Uncertain significance (Nov 06, 2015)
3-196327544-C-T		not specified	Uncertain significance (Sep 22, 2023)
3-196327549-G-GC			Uncertain significance (Mar 31, 2022)
3-196327554-T-C		not specified	Uncertain significance (Dec 09, 2023)
3-196327556-C-T		not specified	Uncertain significance (Apr 26, 2023)
3-196327557-G-A		not specified	Uncertain significance (Sep 22, 2023)
3-196327574-C-A		not specified	Uncertain significance (Mar 21, 2023)
3-196327577-G-T		not specified	Uncertain significance (Sep 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM4SF19	protein_coding	protein_coding	ENST00000273695	4	19162

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000296	0.336	125676	0	70	125746	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.698	94	115	0.817	0.00000597	1317
Missense in Polyphen		41	47.002	0.87231		584
Synonymous	-0.232	52	49.9	1.04	0.00000269	465
Loss of Function	0.323	9	10.1	0.890	5.96e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00312	0.00313
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000880	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.633
• rvis_EVS: 0.9
• rvis_percentile_EVS: 89.39

Haploinsufficiency Scores

• pHI: 0.0651
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0415

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tm4sf19

Gene ontology

• Cellular component: integral component of membrane