MAP7D3

MAP7 domain containing 3

Basic information

Region (hg38): X:136213220-136256482

Links

ENSG00000129680 ∙ NCBI:79649 ∙ OMIM:300930 ∙ HGNC:25742 ∙ Uniprot:Q8IWC1 ∙ 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 MAP7D3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP7D3 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	1	6
missense			55	6	1	62
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	57	11	2

Variants in MAP7D3

This is a list of pathogenic ClinVar variants found in the MAP7D3 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-136219623-C-T		MAP7D3-related disorder	Likely benign (Nov 07, 2019)
X-136220856-G-A		not specified	Uncertain significance (Aug 30, 2024)
X-136220921-G-A		not specified	Uncertain significance (Jun 05, 2023)
X-136220923-C-T		not specified	Likely benign (Feb 07, 2023)
X-136222395-G-A		not specified	Uncertain significance (Jan 08, 2025)
X-136222459-A-G		not specified	Uncertain significance (Sep 09, 2021)
X-136222467-T-C			Uncertain significance (Dec 07, 2021)
X-136222491-G-A			Likely benign (May 30, 2018)
X-136224853-T-C		MAP7D3-related disorder	Uncertain significance (Sep 21, 2024)
X-136224859-G-A		not specified	Uncertain significance (May 21, 2024)
X-136224860-C-T		MAP7D3-related disorder	Likely benign (Jul 12, 2019)
X-136224877-T-C		not specified	Uncertain significance (Feb 27, 2025)
X-136225925-C-T		MAP7D3-related disorder	Benign (Dec 31, 2019)
X-136225967-T-C		not specified	Uncertain significance (Jan 29, 2025)
X-136227302-G-C		not specified	Uncertain significance (Jan 26, 2022)
X-136227340-C-G		not specified	Uncertain significance (Oct 03, 2022)
X-136227388-C-T		not specified	Uncertain significance (Apr 08, 2024)
X-136227405-G-C		not specified	Uncertain significance (Oct 09, 2024)
X-136228631-C-A		not specified	Uncertain significance (Dec 03, 2021)
X-136228641-C-A		not specified	Uncertain significance (Oct 17, 2023)
X-136228641-C-T		not specified	Likely benign (Jan 23, 2025)
X-136228642-G-A		not specified	Uncertain significance (Aug 28, 2024)
X-136228689-C-T		not specified	Uncertain significance (Aug 12, 2021)
X-136228728-A-C		not specified	Uncertain significance (Dec 07, 2021)
X-136230394-T-A		not specified	Uncertain significance (Dec 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP7D3	protein_coding	protein_coding	ENST00000316077	18	43261

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.61e-10	0.810	124707	30	54	124791	0.000337

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.111	342	336	1.02	0.0000265	5765
Missense in Polyphen		59	67.919	0.86868		1321
Synonymous	1.29	108	126	0.855	0.0000109	1610
Loss of Function	1.64	19	28.4	0.669	0.00000195	579

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000939	0.000720
Ashkenazi Jewish	0.00	0.00
East Asian	0.000307	0.000223
Finnish	0.000195	0.000139
European (Non-Finnish)	0.000631	0.000441
Middle Eastern	0.000307	0.000223
South Asian	0.000743	0.000392
Other	0.000225	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes the assembly and stability of microtubules. {ECO:0000269|PubMed:22142902, ECO:0000269|PubMed:24927501}.

Recessive Scores

• pRec: 0.0733

Intolerance Scores

• loftool: 0.983
• rvis_EVS: 0.98
• rvis_percentile_EVS: 90.43

Haploinsufficiency Scores

• pHI: 0.0524
• hipred: N
• hipred_score: 0.123
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0316

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Map7d3

Gene ontology

• Biological process: microtubule cytoskeleton organization;microtubule polymerization
• Cellular component: cytoplasm;spindle;microtubule cytoskeleton;membrane
• Molecular function: microtubule binding;tubulin binding