MAB21L1

mab-21 like 1, the group of MAB21 family

Basic information

Region (hg38): 13:35473419-35478764

Links

ENSG00000180660 ∙ NCBI:4081 ∙ OMIM:601280 ∙ HGNC:6757 ∙ Uniprot:Q13394 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cerebellar, ocular, craniofacial, and genital syndrome (Limited), mode of inheritance: AR
• cerebellar, ocular, craniofacial, and genital syndrome (Strong), mode of inheritance: AR
• cerebellar, ocular, craniofacial, and genital syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cerebellar, ocular, craniofacial, and genital syndrome	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	Craniofacial; Dermatologic; Genitourinary; Neurologic; Ophthalmologic	27075597; 27103078; 30487245

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MAB21L1 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAB21L1 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		1
missense	1		8	1		10
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	1	8	2	0

Variants in MAB21L1

This is a list of pathogenic ClinVar variants found in the MAB21L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-35475279-CG-C		Cerebellar, ocular, craniofacial, and genital syndrome	Pathogenic (Jun 18, 2019)
13-35475296-C-G		Inborn genetic diseases	Uncertain significance (Apr 08, 2024)
13-35475297-TC-T		Cerebellar, ocular, craniofacial, and genital syndrome	Pathogenic (Jun 18, 2019)
13-35475299-G-C		Cerebellar, ocular, craniofacial, and genital syndrome	Pathogenic (Jun 18, 2019)
13-35475319-T-C		MAB21L1-related disorder	Likely benign (Jun 01, 2024)
13-35475337-G-A		Inborn genetic diseases	Uncertain significance (Apr 01, 2024)
13-35475346-G-T		Inborn genetic diseases	Uncertain significance (May 29, 2024)
13-35475367-T-G		MAB21L1-related disorder	Likely benign (Jan 12, 2023)
13-35475401-G-GC		Hypoplasia of scrotum	Likely pathogenic (Jan 01, 2014)
13-35475403-A-AG		Cerebellar, ocular, craniofacial, and genital syndrome	Pathogenic (Jun 18, 2019)
13-35475411-A-G			Uncertain significance (Aug 01, 2023)
13-35475435-G-A		Inborn genetic diseases	Uncertain significance (Apr 12, 2024)
13-35475441-T-G		Cerebellar, ocular, craniofacial, and genital syndrome	Pathogenic (Jun 18, 2019)
13-35475458-G-T		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
13-35475533-C-A		Inborn genetic diseases	Uncertain significance (Oct 17, 2023)
13-35475608-G-A			Likely benign (Jun 01, 2024)
13-35475775-A-T		Inborn genetic diseases	Uncertain significance (Jun 03, 2022)
13-35475922-C-T		Inborn genetic diseases	Uncertain significance (Sep 13, 2023)
13-35475987-C-A			Uncertain significance (Nov 01, 2022)
13-35475987-C-T			Pathogenic (Dec 08, 2022)
13-35476018-C-T			Uncertain significance (-)
13-35476093-A-G		Inborn genetic diseases	Uncertain significance (Apr 06, 2022)
13-35476122-G-A		Inborn genetic diseases	Uncertain significance (Oct 17, 2023)
13-35476878-A-G			Likely benign (Jul 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAB21L1	protein_coding	protein_coding	ENST00000379919	1	2907

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.286	0.710	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	150	193	0.777	0.00000903	2342
Missense in Polyphen		33	72.763	0.45353		867
Synonymous	-2.02	106	82.6	1.28	0.00000410	730
Loss of Function	2.47	3	12.4	0.243	5.47e-7	135

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative nucleotidyltransferase required for several aspects of embryonic development including normal development of the eye (By similarity). It is unclear whether it displays nucleotidyltransferase activity in vivo (PubMed:27271801). Binds single-stranded RNA (ssRNA) (PubMed:27271801). {ECO:0000250|UniProtKB:O70299, ECO:0000269|PubMed:27271801}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.274
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.800
• hipred: Y
• hipred_score: 0.708
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mab21l1
• Phenotype: vision/eye phenotype; renal/urinary system phenotype; pigmentation phenotype; reproductive system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype

Gene ontology

• Biological process: positive regulation of cell population proliferation;anatomical structure morphogenesis;camera-type eye development
• Cellular component: nucleus
• Molecular function: protein binding;ATP binding;GTP binding;nucleotidyltransferase activity;metal ion binding