GPANK1

Chr 6

G-patch domain and ankyrin repeats 1

Also known as: ANKRD59, BAT4, D6S54E, G5, GPATCH10

NCBI Gene: 7918 ENSG00000204438 UniProt: O95872 OMIM: 142610

The GPANK1 protein is thought to function in immunity and is located within the major histocompatibility complex III region. Mutations cause autosomal recessive spastic paraplegia with intellectual disability, seizures, and progressive neurodegeneration typically beginning in early childhood. The gene is not highly constrained against loss-of-function variation.

OMIM ResearchSummary from RefSeq

This gene is located in a cluster of HLA-B-associated transcripts, which is included in the human major histocompatability complex III region. This gene encodes a protein which is thought to play a role in immunity. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Nov 2010]

OMIM ResearchGenerating clinical summary…

LOEUF 1.40

Clinical Summary— GPANK1

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

68 VUS of 77 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.40LOEUF

pLI 0.000

Z-score 0.51

OE 0.85 (0.53–1.40)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.42Z-score

OE missense 0.92 (0.81–1.03)

189 obs / 206.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.85 (0.53–1.40)

0≤0.351.4

Missense OE?0.92 (0.81–1.03)

0≤0.61.4

Synonymous OE?0.84

0≤1.21.6

LoF obs/exp: 11 / 13.0Missense obs/exp: 189 / 206.1Syn Z: 1.13

ClinVar Variant Classifications

77 submitted variants in ClinVar

ClinVar

Classification Summary

VUS68

Likely Benign4

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	68	0	68
Likely Benign	3	1	4
Benign	0	0	0
Total	71	1	72

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

9 pathogenic / likely-pathogenic (of 13) ClinVar copy-number / structural variants overlap GPANK1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →