MAP6D1

protein-coding

MAP6 domain containing 1

Gene summary

This gene encodes a protein highly similar to the mouse MAP6 domain containing 1 protein, which is related to the STOP proteins. Based on the study of the mouse protein, the encoded protein may function as a calmodulin-regulated neuronal protein that binds and stabilizes microtubules but also associates with the Golgi membranes through N-terminal palmitoylation. [provided by RefSeq, Oct 2008]

MANE transcript

NM_024871.4

Inheritance

—

ClinVar variants

U:41B:7

Top phenotype

MAP6D1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr3:183,815,922-183,825,594

External References & Databases

Ensembl (ENSG00000180834)

Transcript & Mutation Effects

hg38 • Region Span ~9.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MAP6D1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

MAP6D1-related disorderTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024871.4. 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				4 clinvar	1 clinvar	5
missense			41 clinvar	1 clinvar	1 clinvar	43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	5	2	48

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024871.4	RefSeq	NP_079147.1	3	MANE Select
ENST00000318631.8	Ensembl	ENSP00000314560.4	3	MANE Select
ENST00000431348.1	Ensembl	ENSP00000388945.1	3	Standard
ENST00000445426.1	Ensembl	ENSP00000390816.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

microtubule cytoskeleton organization
negative regulation of microtubule depolymerization
N-terminal peptidyl-L-cysteine N-palmitoylation
cytoskeleton-dependent intracellular transport
regulation of microtubule cytoskeleton organization

Molecular Function

calmodulin binding
microtubule binding

Cellular Component

Golgi-associated vesicle
cis-Golgi network
microtubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000318631
Coding exons: 3
Length: 9719
Individuals with no LoFs: 125724
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125730
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.175	59	55.3	1.07	0.00000297	1162
Missense (PolyPhen)		19	20.697	0.918		465
Synonymous	0.570	20	23.5	0.850	0.00000138	429
Loss of Function	1.28	2	5.12	0.391	3.05e-7	68

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May have microtubule-stabilizing activity. {ECO:0000250}.;

Recessive Scores

pRec: 0.0872

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0169

Gene Damage Prediction

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