MAP7D3

protein-coding

MAP7 domain containing 3

Gene summary

The protein encoded by this gene belongs to the MAP7 (microtubule-associated protein 7) family. Alternatively spliced transcript variants encoding different isoforms have been found. [provided by RefSeq, Mar 2010]

MANE transcript

NM_024597.4

Inheritance

ClinVar variants

U:224B:27

Top phenotype

MAP7D3-related disorder

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chrX:136,213,220-136,256,482

External References & Databases

Ensembl (ENSG00000129680)

Transcript & Mutation Effects

hg38 • Region Span ~43.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderLIMITED

Inheritance Pattern: XL

Disease ID:MONDO:0700092

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MAP7D3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 110

not providedTotal: 20

MAP7D3-related disorderTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024597.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			16 clinvar	10 clinvar	1 clinvar	27
missense			172 clinvar	13 clinvar	3 clinvar	188
nonsense			15 clinvar			15
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			20 clinvar			20
Total	0	0	224	23	4	251

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024597.4	RefSeq	NP_078873.2	18	MANE Select
ENST00000316077.14	Ensembl	ENSP00000318086.9	18	MANE Select
NM_001173516.1	RefSeq	NP_001166987.1	18	Standard
NM_001173517.2	RefSeq	NP_001166988.1	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

microtubule cytoskeleton organization
microtubule polymerization

Molecular Function

microtubule binding
tubulin binding

Cellular Component

cytoplasm
spindle
microtubule cytoskeleton
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000316077
Coding exons: 18
Length: 43261
Individuals with no LoFs: 124707
Homozygous LoFs: 30
Heterozygous LoFs: 54
Defined: 124791
p: 0.000337

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.111	342	336	1.02	0.0000265	5765
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00067	0.00045	rare
Latino/Admixed American	0.00027	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00031	0.00022	rare
Finnish	0.00019	0.00014	rare
European (Non-Finnish)	0.00063	0.00044	rare
South Asian	0.00074	0.00039	rare
Other	0.00022	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0316

Gene Damage Prediction

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