TMEM14B

transmembrane protein 14B, the group of Transmembrane protein 14 family

Basic information

Region (hg38): 6:10747759-10852753

Links

ENSG00000137210 ∙ NCBI:81853 ∙ OMIM:619865 ∙ HGNC:21384 ∙ Uniprot:Q9NUH8 ∙ 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 TMEM14B gene.

• not provided (54 variants)
• Retinitis pigmentosa (4 variants)
• Retinitis pigmentosa 62 (2 variants)
• Retinal dystrophy (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM14B 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2			2
non coding	57	22	222	241	15	557
Total	57	22	228	242	15

Highest pathogenic variant AF is 0.0000526

Variants in TMEM14B

This is a list of pathogenic ClinVar variants found in the TMEM14B region.

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

Position	Type	Phenotype	Significance	ClinVar
6-10749656-G-A		not specified	Uncertain significance (May 03, 2023)
6-10749657-C-T		not specified	Uncertain significance (May 10, 2024)
6-10749669-C-T		not specified	Uncertain significance (Aug 12, 2021)
6-10749680-G-A		not specified	Likely benign (Nov 13, 2023)
6-10751180-G-A		not specified	Uncertain significance (Jul 20, 2021)
6-10751193-A-T		not specified	Uncertain significance (Dec 19, 2022)
6-10751223-G-C		not specified	Uncertain significance (Sep 07, 2022)
6-10756496-G-A		not specified	Uncertain significance (Nov 14, 2023)
6-10762764-G-T		Retinitis Pigmentosa, Recessive	Benign (Jun 14, 2016)
6-10762889-C-T		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
6-10763013-CAGT-C		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
6-10763023-CATT-C		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
6-10763079-G-A		Retinitis Pigmentosa, Recessive	Benign (Jun 14, 2016)
6-10763105-G-A		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
6-10763486-G-A		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
6-10763546-TA-T		Retinitis Pigmentosa, Recessive	Benign (Jun 14, 2016)
6-10763724-G-A		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
6-10763850-C-CA		Retinitis Pigmentosa, Recessive	Likely benign (Jun 14, 2016)
6-10764119-C-CTA		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
6-10764139-G-GTT		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
6-10764173-T-G		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
6-10764226-C-T		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
6-10764418-G-A		Retinitis Pigmentosa, Recessive	Uncertain significance (Jun 14, 2016)
6-10764452-C-T			Likely benign (Oct 31, 2023)
6-10764455-C-T			Likely benign (Mar 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM14B	protein_coding	protein_coding	ENST00000379542	5	104995

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.72e-9	0.0261	125624	1	122	125747	0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.495	80	68.5	1.17	0.00000381	722
Missense in Polyphen		19	18.16	1.0463		240
Synonymous	0.269	23	24.7	0.931	0.00000149	233
Loss of Function	-1.48	10	6.06	1.65	2.57e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00177	0.00177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000272	0.000272
South Asian	0.00261	0.00258
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Primate-specific protein involved in cortical expansion and folding in the developing neocortex. May drive neural progenitor proliferation through nuclear translocation of IQGAP1, which in turn promotes G1/S cell cycle transitions. {ECO:0000269|PubMed:29033352}.

Recessive Scores

• pRec: 0.0709

Intolerance Scores

• loftool: 0.883
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.139
• ghis: 0.619

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0248

Gene Damage Prediction

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

Zebrafish Information Network

• Gene name: tmem14ca
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: cerebral cortex development;neural precursor cell proliferation;regulation of G1/S transition of mitotic cell cycle
• Cellular component: integral component of membrane
• Molecular function: protein binding