MFAP3L

microfibril associated protein 3 like, the group of I-set domain containing

Basic information

Region (hg38): 4:169986597-170033031

Links

ENSG00000198948 ∙ NCBI:9848 ∙ OMIM:616523 ∙ HGNC:29083 ∙ Uniprot:O75121 ∙ 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 MFAP3L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MFAP3L 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			18	3		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	0

Variants in MFAP3L

This is a list of pathogenic ClinVar variants found in the MFAP3L region.

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

Position	Type	Phenotype	Significance	ClinVar
4-169991565-A-G		not specified	Likely benign (Sep 28, 2021)
4-169991619-G-A		not specified	Likely benign (Feb 15, 2023)
4-169991659-T-C		not specified	Uncertain significance (Jul 25, 2023)
4-169991695-C-A		not specified	Uncertain significance (Jul 12, 2022)
4-169991767-C-T		not specified	Likely benign (Jun 06, 2022)
4-169991770-C-T		not specified	Uncertain significance (Sep 20, 2023)
4-169991884-G-T		not specified	Uncertain significance (Dec 13, 2023)
4-169991887-C-T		not specified	Uncertain significance (Jul 09, 2021)
4-169991913-C-T		not specified	Uncertain significance (Jan 02, 2024)
4-169991933-G-T		not specified	Uncertain significance (Dec 12, 2023)
4-169991968-C-T		not specified	Uncertain significance (Mar 14, 2023)
4-169991991-T-C		not specified	Uncertain significance (May 18, 2023)
4-169992054-G-A		not specified	Uncertain significance (Mar 19, 2024)
4-169992058-T-C		not specified	Uncertain significance (Dec 17, 2023)
4-169992090-C-T		not specified	Uncertain significance (Apr 20, 2023)
4-169992286-C-T		not specified	Uncertain significance (Aug 09, 2021)
4-169992292-C-T		not specified	Uncertain significance (Nov 07, 2022)
4-170005706-C-T		not specified	Uncertain significance (Feb 28, 2023)
4-170005723-C-T		not specified	Uncertain significance (Jan 08, 2024)
4-170005736-C-T		not specified	Uncertain significance (Mar 30, 2024)
4-170005757-C-T		not specified	Uncertain significance (Aug 02, 2021)
4-170005778-T-C		not specified	Uncertain significance (Aug 09, 2021)
4-170005807-G-A		not specified	Uncertain significance (Jul 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MFAP3L	protein_coding	protein_coding	ENST00000361618	2	46435

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.880	0.119	125726	0	7	125733	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	181	243	0.744	0.0000145	2685
Missense in Polyphen		51	100.99	0.50498		1048
Synonymous	-0.563	115	108	1.07	0.00000769	832
Loss of Function	2.84	1	11.3	0.0885	6.35e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May participate in the nuclear signaling of EGFR and MAPK1/ERK2. May a have a role in metastasis. {ECO:0000269|PubMed:24735981}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.0592
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• pHI: 0.542
• hipred: Y
• hipred_score: 0.707
• ghis: 0.601

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.140

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mfap3l

Gene ontology

• Cellular component: nucleus;cytoplasm;plasma membrane;integral component of membrane
• Molecular function: protein binding