POC1B-GALNT4

POC1B-GALNT4 readthrough

Basic information

Region (hg38): 12:89519408-89526262

Links

ENSG00000259075 ∙ NCBI:100528030 ∙ ∙ HGNC:42957 ∙ ∙ ∙ 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 POC1B-GALNT4 gene.

• not provided (39 variants)
• Inborn genetic diseases (5 variants)
• Childhood-onset schizophrenia (1 variants)
• Cone-rod dystrophy 20 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POC1B-GALNT4 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		1		2		3
missense			19	1	1	21
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1	2	2		5
splice region						0
non coding			2	12	2	16
Total	0	3	23	17	3

Variants in POC1B-GALNT4

This is a list of pathogenic ClinVar variants found in the POC1B-GALNT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-89522853-T-C		not specified	Uncertain significance (Aug 12, 2021)
12-89522878-G-A		not specified	Uncertain significance (Dec 08, 2023)
12-89522880-C-T		not specified	Uncertain significance (Dec 13, 2022)
12-89522895-C-T		not specified	Uncertain significance (Aug 08, 2022)
12-89522907-A-G		not specified	Uncertain significance (Apr 11, 2023)
12-89523004-G-T			Benign/Likely benign (Oct 01, 2023)
12-89523118-G-A		not specified	Uncertain significance (Jun 16, 2023)
12-89523201-C-A		not specified	Uncertain significance (Aug 02, 2023)
12-89523202-T-C		not specified	Uncertain significance (Sep 22, 2023)
12-89523206-A-C		not specified	Uncertain significance (Jul 26, 2022)
12-89523218-C-A		not specified	Uncertain significance (Jan 05, 2022)
12-89523250-T-C		not specified	Uncertain significance (Sep 22, 2022)
12-89523297-C-T		not specified	Uncertain significance (Aug 27, 2024)
12-89523356-G-A		Childhood-onset schizophrenia	Likely pathogenic (Jan 01, 2014)
12-89523366-T-C		not specified	Uncertain significance (May 24, 2023)
12-89523450-C-T		not specified	Uncertain significance (Mar 06, 2023)
12-89523453-T-C		not specified	Uncertain significance (Jun 30, 2022)
12-89523565-T-C		not specified	Uncertain significance (May 11, 2022)
12-89523572-C-T			Likely benign (Dec 01, 2022)
12-89523726-A-G		not specified	Uncertain significance (Feb 23, 2023)
12-89523764-A-T			Benign (Jun 23, 2018)
12-89523783-A-G		not specified	Uncertain significance (Jun 06, 2023)
12-89523832-G-C		not specified	Uncertain significance (May 23, 2023)
12-89523886-C-T		not specified	Uncertain significance (Oct 03, 2022)
12-89523925-T-C		not specified	Uncertain significance (Dec 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POC1B-GALNT4	protein_coding	protein_coding	ENST00000548729	3	6855

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.107	0.893	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0621	317	320	0.990	0.0000165	3763
Missense in Polyphen		145	160.01	0.9062		1826
Synonymous	-0.447	123	117	1.05	0.00000591	1106
Loss of Function	3.20	6	22.3	0.269	0.00000126	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000375	0.000240
Ashkenazi Jewish	0.00	0.00
East Asian	0.000281	0.000272
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000365	0.000360
Middle Eastern	0.000281	0.000272
South Asian	0.000131	0.000131
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D- galactosamine residue to a serine or threonine residue on the protein receptor. Has a highest activity toward Muc7, EA2 and Muc2, with a lowest activity than GALNT2. Glycosylates 'Thr-57' of SELPLG.
• Pathway: Mucin type O-glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;mucin core 1 and core 2 <i>O</i>-glycosylation;O-Glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Intolerance Scores

• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.41

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.273
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene ontology

• Biological process: protein glycosylation
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane
• Molecular function: transferase activity, transferring glycosyl groups;carbohydrate binding