PMF1-BGLAP

PMF1-BGLAP readthrough

Basic information

Region (hg38): 1:156212981-156243332

Links

ENSG00000260238 ∙ NCBI:100527963 ∙ ∙ HGNC:42953 ∙ ∙ ∙ 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 PMF1-BGLAP gene.

• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PMF1-BGLAP 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in PMF1-BGLAP

This is a list of pathogenic ClinVar variants found in the PMF1-BGLAP region.

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

Position	Type	Phenotype	Significance	ClinVar
1-156213157-A-C		not specified	Uncertain significance (Aug 17, 2022)
1-156225579-G-A		not specified	Uncertain significance (Aug 21, 2023)
1-156225594-C-T		not specified	Uncertain significance (Aug 02, 2022)
1-156225613-A-G		not specified	Uncertain significance (Jun 03, 2022)
1-156225640-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-156232418-C-A		not specified	Uncertain significance (May 05, 2023)
1-156236298-G-A		not specified	Uncertain significance (Feb 22, 2023)
1-156236426-G-C		not specified	Uncertain significance (Feb 28, 2023)
1-156236427-C-T		Inborn genetic diseases	Uncertain significance (Mar 20, 2023)
1-156242282-C-T			Likely benign (Mar 01, 2022)
1-156242556-C-T		not specified	Uncertain significance (May 31, 2023)
1-156242567-G-A		not specified	Uncertain significance (Mar 06, 2023)
1-156242577-C-A		not specified	Uncertain significance (Sep 22, 2022)
1-156242814-C-G		not specified	Uncertain significance (Mar 02, 2023)
1-156242823-A-G		not specified	Uncertain significance (Jul 20, 2021)
1-156243037-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-156243120-C-G		not specified	Uncertain significance (Aug 21, 2023)
1-156243121-G-A		not specified	Uncertain significance (Aug 11, 2022)
1-156243139-C-T		not specified	Uncertain significance (Jun 28, 2022)
1-156243140-G-A			Benign (Dec 31, 2019)
1-156243151-G-A		not specified	Uncertain significance (Jan 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PMF1-BGLAP	protein_coding	protein_coding	ENST00000368276	7	30351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.07e-8	0.184	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.346	140	129	1.09	0.00000677	1427
Missense in Polyphen		34	42.394	0.80199		491
Synonymous	0.0217	50	50.2	0.996	0.00000288	404
Loss of Function	0.326	13	14.3	0.907	6.97e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000418	0.000412
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000178	0.000176
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of the MIS12 complex which is required for normal chromosome alignment and segregation and kinetochore formation during mitosis. May act as a cotranscription partner of NFE2L2 involved in regulation of polyamine-induced transcription of SSAT. {ECO:0000269|PubMed:10419538, ECO:0000269|PubMed:11256947, ECO:0000269|PubMed:15502821, ECO:0000269|PubMed:16585270}.

Intolerance Scores

• rvis_EVS: 0.77
• rvis_percentile_EVS: 87.06

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N

Gene ontology

• Cellular component: nuclear MIS12/MIND complex;nucleoplasm;Golgi apparatus;intracellular membrane-bounded organelle