PMFBP1

polyamine modulated factor 1 binding protein 1

Basic information

Region (hg38): 16:72112157-72176878

Links

ENSG00000118557 ∙ NCBI:83449 ∙ OMIM:618085 ∙ HGNC:17728 ∙ Uniprot:Q8TBY8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 31 (Limited), mode of inheritance: AR
• spermatogenic failure 31 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 31	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	30032984

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PMFBP1 gene.

• Spermatogenic failure 31 (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PMFBP1 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				5		5
missense			60	5	6	71
nonsense	2	2				4
start loss						0
frameshift	1					1
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding					2	2
Total	3	2	60	11	8

Highest pathogenic variant AF is 0.0000197

Variants in PMFBP1

This is a list of pathogenic ClinVar variants found in the PMFBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-72112393-C-G			Likely benign (Mar 14, 2023)
16-72112397-C-T			Likely benign (Aug 30, 2023)
16-72112403-G-C			Likely benign (Jul 14, 2022)
16-72112410-C-A			Uncertain significance (Jan 21, 2020)
16-72112418-C-T		not specified	Uncertain significance (Jul 25, 2022)
16-72112423-A-T			Uncertain significance (Oct 13, 2022)
16-72112431-T-G			Likely benign (Dec 12, 2021)
16-72112437-C-T			Likely benign (Sep 03, 2022)
16-72112438-C-A			Likely benign (Jan 03, 2022)
16-72112438-C-T			Uncertain significance (Jun 07, 2022)
16-72112443-A-G			Likely benign (Nov 22, 2022)
16-72112445-A-T			Uncertain significance (Feb 10, 2022)
16-72112450-G-A			Uncertain significance (Aug 15, 2022)
16-72112455-G-A			Likely benign (Oct 17, 2022)
16-72112464-C-A			Likely benign (Aug 10, 2023)
16-72112468-C-G			Uncertain significance (Jun 20, 2022)
16-72112468-C-T			Uncertain significance (Aug 23, 2022)
16-72112469-G-A			Uncertain significance (Nov 08, 2022)
16-72112469-G-C		not specified	Uncertain significance (Apr 28, 2023)
16-72112475-C-T		DHX38-related disorder	Likely benign (Jan 29, 2024)
16-72112476-G-A			Likely benign (Oct 24, 2023)
16-72112484-G-A			Uncertain significance (Jun 28, 2022)
16-72112485-C-T			Likely benign (Oct 20, 2022)
16-72119336-T-A		PMFBP1-related disorder	Benign (Jul 16, 2019)
16-72119342-C-T		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PMFBP1	protein_coding	protein_coding	ENST00000237353	20	64722

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.34e-34	0.000312	125283	0	465	125748	0.00185

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.468	552	522	1.06	0.0000274	6710
Missense in Polyphen		136	131.53	1.034		1992
Synonymous	-1.19	234	212	1.10	0.0000120	1726
Loss of Function	0.857	55	62.3	0.883	0.00000320	729

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00221	0.00222
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00903	0.00907
Finnish	0.00208	0.00208
European (Non-Finnish)	0.00121	0.00120
Middle Eastern	0.00903	0.00907
South Asian	0.00157	0.00154
Other	0.00245	0.00245

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in sperm morphology especially the sperm tail and consequently affect fertility. May also be involved in the general organization of cellular cytoskeleton. {ECO:0000269|PubMed:1770140}.

Intolerance Scores

• loftool: 0.996
• rvis_EVS: -0.66
• rvis_percentile_EVS: 16.12

Haploinsufficiency Scores

• pHI: 0.130
• 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: 0.188

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Pmfbp1

Gene ontology

• Biological process: spermatogenesis;biological_process
• Cellular component: cytoplasm;sperm connecting piece
• Molecular function: molecular_function