FRMPD3

FERM and PDZ domain containing 3, the group of PDZ domain containing|FERM domain containing

Basic information

Region (hg38): X:107449652-107605255

Links

ENSG00000147234 ∙ NCBI:84443 ∙ OMIM:301005 ∙ HGNC:29382 ∙ Uniprot:Q5JV73 ∙ 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 FRMPD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FRMPD3 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				7		7
missense				4		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	11	0

Variants in FRMPD3

This is a list of pathogenic ClinVar variants found in the FRMPD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-107533543-C-G			Likely benign (Dec 01, 2022)
X-107597963-G-A			Likely benign (May 01, 2023)
X-107600415-C-T			Likely benign (Mar 01, 2020)
X-107600543-G-T		Abnormality of neuronal migration	Benign (Oct 31, 2014)
X-107600836-C-T			Likely benign (Jun 01, 2022)
X-107602090-C-T			Likely benign (Jan 01, 2023)
X-107602098-T-C			Likely benign (Nov 01, 2022)
X-107602107-C-G		Low-frequency hearing loss;Low-frequency sensorineural hearing impairment	Likely benign (May 13, 2022)
X-107602455-C-T			Likely benign (Jun 01, 2022)
X-107602872-C-T			Likely benign (Jan 01, 2023)
X-107602969-C-T			Uncertain significance (-)
X-107603211-G-A			Likely benign (Feb 01, 2024)
X-107603244-A-G			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FRMPD3	protein_coding	protein_coding	ENST00000276185	16	82802

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000190	1.00	122742	4	20	122766	0.0000978

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	664	742	0.895	0.0000620	11742
Missense in Polyphen		189	250.34	0.75498		3786
Synonymous	1.68	258	295	0.876	0.0000237	3790
Loss of Function	4.63	17	53.6	0.317	0.00000478	741

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000110	0.000110
Ashkenazi Jewish	0.000277	0.000200
East Asian	0.000224	0.000165
Finnish	0.0000666	0.0000463
European (Non-Finnish)	0.000189	0.000128
Middle Eastern	0.000224	0.000165
South Asian	0.0000532	0.0000329
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.384
• ghis: 0.463

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.164

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Frmpd3

Gene ontology

• Biological process: neutrophil degranulation
• Cellular component: cytoskeleton;plasma membrane;secretory granule membrane;tertiary granule membrane